def test_simple_input(self):
# Reference structure
s = ("acell 1 1 1 rprim 1 0 0 0 1 0 0 0 1 natom 1 "
"ntypat 1 typat 1 znucl 14 xred 0 0 0 ")
inp = AbinitInputFile.from_string(s)
print(inp)
si1_structure = inp.structure
assert inp.ndtset == 1 and len(
si1_structure) == 1 and si1_structure.formula == "Si1"
# Default values for acell (3*1) and rprim (np.eye(3))
s = "natom 1 ntypat 1 typat 1 znucl 14 xred 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# Same structure but with * syntax.
s = "acell 3*1 natom 1 ntypat 1 typat 1 znucl 14 xred 3*0e0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# xcart instead of xred and more variables using * syntax.
s = "acell 1 2*1 natom 1*1 ntypat 1*1 typat 1*1 znucl *14 xcart 0d0 0d0 0d0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# acell and rprimd with unit.
s = ("acell 1 2*1 Bohr rprim 1 0 0 0 1 0 0 0 1 Bohr natom 1 "
"ntypat 1 typat *1 znucl 1*14 xangst 0 0 0")
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
def test_input_with_serie(self):
# Test arithmetic and geometric series with ecut.
s = """
ndtset 3
natom 2 ntypat 1 znucl 1 typat 2*1
acell 10 10 10 xcart -0.7 0.0 0.0 0.7 0.0 0.0
ecut: 10 ecut+ 5
pawecutdg: 2 pawecutdg* 3
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 3
self.assertArrayEqual([dt["ecut"] for dt in inp.datasets],
[10, 15, 20])
self.assertArrayEqual([dt["pawecutdg"] for dt in inp.datasets],
[2, 6, 18])
print(inp)
# Test arithmetic series with xcart.
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell 1 1 1
xcart: -0.7 0.0 0.0 0.7 0.0 0.0
xcart+ -0.1 0.0 0.0 0.1 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2 and inp.structure is None
s0, s1 = inp.datasets[0].structure, inp.datasets[1].structure
self.assert_almost_equal(s0.cart_coords.ravel() / bohr_to_ang,
[-0.7, 0, 0, 0.7, 0, 0])
self.assert_almost_equal(s1.cart_coords.ravel() / bohr_to_ang,
[-0.8, 0, 0, 0.8, 0, 0])
print(inp)
def test_simple_input(self):
# Reference structure
s = ("acell 1 1 1 rprim 1 0 0 0 1 0 0 0 1 natom 1 "
"ntypat 1 typat 1 znucl 14 xred 0 0 0 ")
inp = AbinitInputFile.from_string(s)
repr(inp); str(inp)
assert inp.to_string(verbose=1)
assert inp._repr_html_()
si1_structure = inp.structure
assert inp.ndtset == 1 and len(si1_structure) == 1 and si1_structure.formula == "Si1"
# Default values for acell (3*1) and rprim (np.eye(3))
s = "natom 1 ntypat 1 typat 1 znucl 14 xred 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# Same structure but with * syntax.
s = "acell 3*1 natom 1 ntypat 1 typat 1 znucl 14 xred 3*0e0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
assert not inp.has_multi_structures
# xcart instead of xred and more variables using * syntax.
s = "acell 1 2*1 natom 1*1 ntypat 1*1 typat 1*1 znucl *14 xcart 0d0 0d0 0d0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# acell and rprimd with unit.
s = ("acell 1 2*1 Bohr rprim 1 0 0 0 1 0 0 0 1 Bohr natom 1 "
"ntypat 1 typat *1 znucl 1*14 xangst 0 0 0")
with AbinitInputFile.from_string(s) as inp:
assert inp.structure == si1_structure
if self.has_nbformat():
inp.write_notebook(nbpath=self.get_tmpname(text=True))
def test_input_with_serie(self):
# Test arithmetic and geometric series with ecut.
s = """
ndtset 3
natom 2 ntypat 1 znucl 1 typat 2*1
acell 10 10 10 xcart -0.7 0.0 0.0 0.7 0.0 0.0
ecut: 10 ecut+ 5
pawecutdg: 2 pawecutdg* 3
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 3
self.assertArrayEqual([dt["ecut"] for dt in inp.datasets], [10, 15, 20])
self.assertArrayEqual([dt["pawecutdg"] for dt in inp.datasets], [2, 6, 18])
repr(inp); str(inp)
# Test arithmetic series with xcart.
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell 1 1 1
xcart: -0.7 0.0 0.0 0.7 0.0 0.0
xcart+ -0.1 0.0 0.0 0.1 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2 and inp.structure is None
s0, s1 = inp.datasets[0].structure, inp.datasets[1].structure
self.assert_almost_equal(s0.cart_coords.ravel() / bohr_to_ang, [-0.7, 0, 0, 0.7, 0, 0])
self.assert_almost_equal(s1.cart_coords.ravel() / bohr_to_ang, [-0.8, 0, 0, 0.8, 0, 0])
str(inp)
def test_simple_input(self):
# Reference structure
s = ("acell 1 1 1 rprim 1 0 0 0 1 0 0 0 1 natom 1 "
"ntypat 1 typat 1 znucl 14 xred 0 0 0 ")
inp = AbinitInputFile.from_string(s)
repr(inp)
str(inp)
assert inp.to_string(verbose=1)
assert inp._repr_html_()
si1_structure = inp.structure
assert inp.ndtset == 1 and len(
si1_structure) == 1 and si1_structure.formula == "Si1"
# Default values for acell (3*1) and rprim (np.eye(3))
s = "natom 1 ntypat 1 typat 1 znucl 14 xred 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# Same structure but with * syntax.
s = "acell 3*1 natom 1 ntypat 1 typat 1 znucl 14 xred 3*0e0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# xcart instead of xred and more variables using * syntax.
s = "acell 1 2*1 natom 1*1 ntypat 1*1 typat 1*1 znucl *14 xcart 0d0 0d0 0d0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# acell and rprimd with unit.
s = ("acell 1 2*1 Bohr rprim 1 0 0 0 1 0 0 0 1 Bohr natom 1 "
"ntypat 1 typat *1 znucl 1*14 xangst 0 0 0")
with AbinitInputFile.from_string(s) as inp:
assert inp.structure == si1_structure
if self.has_nbformat():
inp.write_notebook(nbpath=self.get_tmpname(text=True))
def test_simple_input(self):
# Reference structure
s = ("acell 1 1 1 rprim 1 0 0 0 1 0 0 0 1 natom 1"
"ntypat 1 typat 1 znucl 14 xred 0 0 0")
inp = AbinitInputFile.from_string(s)
print(inp)
si1_structure = inp.structure
assert inp.ndtset == 1 and len(si1_structure) == 1 and si1_structure.formula == "Si1"
# Default values for acell (3*1) and rprim (np.eye(3))
s = "natom 1" "ntypat 1 typat 1 znucl 14 xred 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# Same structure but with * syntax.
s = "acell 3*1 natom 1 ntypat 1 typat 1 znucl 14 xred 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# xcart instead of xred and more variables using * syntax.
s = "acell 1 2*1 natom 1*1 ntypat 1*1 typat 1*1 znucl 1*14 xcart 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
# acell and rprimd with unit.
s = "acell 1 2*1 Bohr rprim 1 0 0 0 1 0 0 0 1 Bohr natom 1*1 ntypat 1*1 typat 1*1 znucl 1*14 xangst 0 0 0"
inp = AbinitInputFile.from_string(s)
assert inp.structure == si1_structure
def test_input_with_datasets(self):
# H2 molecule in a big box
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell1 10 10 10 # this is a comment
acell2 20 20 20
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2
dt0 = inp.datasets[0]
repr(dt0)
str(dt0)
assert dt0.to_string(verbose=2)
assert dt0._repr_html_()
s0, s1 = inp.datasets[0].structure, inp.datasets[1].structure
assert s0 != s1
assert s1.volume == 8 * s0.volume
repr(inp)
str(inp)
# same input but with global acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell 10 10 10 ! this is a comment
acell2 20 20 20 ! bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
repr(inp)
str(inp)
d = inp.datasets[1].get_vars()
assert "natom" not in d and len(d) == 0
# same input in terms of an arithmetic series in acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell: 10 10 10
acell+ 10 10 10 # bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
str(inp)
def test_input_with_datasets(self):
# H2 molecule in a big box
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell1 10 10 10 # this is a comment
acell2 20 20 20
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2
dt0 = inp.datasets[0]
repr(dt0); str(dt0)
assert dt0.to_string(verbose=2)
assert dt0._repr_html_()
s0, s1 = inp.datasets[0].structure, inp.datasets[1].structure
assert s0 != s1
assert s1.volume == 8 * s0.volume
repr(inp); str(inp)
# same input but with global acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell 10 10 10 ! this is a comment
acell2 20 20 20 ! bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
repr(inp); str(inp)
d = inp.datasets[1].get_vars()
assert "natom" not in d and len(d) == 0
# same input in terms of an arithmetic series in acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell: 10 10 10
acell+ 10 10 10 # bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
str(inp)
def test_input_with_datasets(self):
# H2 molecule in a big box
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell1 10 10 10 # this is a comment
acell2 20 20 20
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2
s0, s1 = inp.datasets[0].structure, inp.datasets[1].structure
assert s0 != s1
assert s1.volume == 8 * s0.volume
print(inp)
# same input but with global acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell 10 10 10 ! this is a comment
acell2 20 20 20 ! bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
print(inp)
# same input in terms of an arithmetic series in acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell: 10 10 10
acell+ 10 10 10 # bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
print(inp)
def test_input_with_datasets(self):
# H2 molecule in a big box
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell1 10 10 10 # this is a comment
acell2 20 20 20
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2
s0, s1 = inp.datasets[0].structure, inp.datasets[1].structure
assert s0 != s1
assert s1.volume == 8 * s0.volume
print(inp)
# same input but with global acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell 10 10 10 ! this is a comment
acell2 20 20 20 ! bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
print(inp)
# same input in terms of an arithmetic series in acell
s = """
ndtset 2
natom 2 ntypat 1 znucl 1 typat 2*1
acell: 10 10 10
acell+ 10 10 10 # bohrs
xcart -0.7 0.0 0.0 0.7 0.0 0.0
"""
inp = AbinitInputFile.from_string(s)
assert s0 == inp.datasets[0].structure
assert s1 == inp.datasets[1].structure
print(inp)
def test_tricky_inputs(self):
"""Testing tricky inputs"""
s = """\
# define kpt mesh
kptrlatt 2 2 -2
-2 2 -2
-2 2 2
#definition of the elementary cell
natom 2
ntypat 2
znucl 31 1*33
typat 1*1 2
acell 3*5.6533 angstrom # expt value
rprim 0 1/2 1/2
1/2 0 1/2
1/2 1/2 0
include "foo"
xred 3*0 3*1/4
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 1 and inp.structure is not None and len(
inp.structure) == 2
self.assertArrayEqual(inp.structure[0].frac_coords, [0, 0, 0])
self.assertArrayEqual(inp.structure[0].specie.symbol, "Ga")
self.assertArrayEqual(inp.structure[1].frac_coords,
[1 / 4, 1 / 4, 1 / 4])
self.assertArrayEqual(inp.structure[1].specie.symbol, "As")
mat = 5.6533 * np.array(
[0, 1 / 2, 1 / 2, 1 / 2, 0, 1 / 2, 1 / 2, 1 / 2, 0])
mat.shape = (3, 3)
self.assertArrayEqual(inp.structure[1].lattice.matrix, mat)
# tutorial/input/tbase2_1
# 2 datasets with different natom (should use typat[:1] in 2nd dataset)
s = """\
ndtset 2
#Definition of the unit cell and ecut,
#for which one will have to make a convergence study
acell 10 10 10
ecut 10
natom1 2 # There are two atoms
xcart1 -0.7 0.0 0.0 # The starting values of the
0.7 0.0 0.0 # atomic coordinates
#Second dataset : get the total energy of the isolated atom
natom2 1 # There is one atom
xcart2 0.0 0.0 0.0 # The atom is located at the origin
#Definition of the atom types
ntypat 1 # There is only one type of atom
znucl 1 # The keyword "znucl" refers to the atomic number of the
#Definition of the atoms
typat 1 1 # For the first dataset, both numbers will be read,
# while for the second dataset, only one number will be read
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2 and inp.structure is None
assert len(inp.datasets[0].structure) == 2
assert len(inp.datasets[1].structure) == 1
print(inp)
def test_tricky_inputs(self):
"""Testing tricky inputs"""
s = """\
# define kpt mesh
kptrlatt 2 2 -2
-2 2 -2
-2 2 2
#definition of the elementary cell
natom 2
ntypat 2
znucl 31 1*33
typat 1*1 2
acell 3*5.6533 angstrom # expt value
rprim 0 1/2 1/2
1/2 0 1/2
1/2 1/2 0
include "foo"
xred 3*0 3*1/4
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 1 and inp.structure is not None and len(inp.structure) == 2
self.assertArrayEqual(inp.structure[0].frac_coords, [0, 0, 0])
self.assertArrayEqual(inp.structure[0].specie.symbol, "Ga")
self.assertArrayEqual(inp.structure[1].frac_coords, [1/4, 1/4, 1/4])
self.assertArrayEqual(inp.structure[1].specie.symbol, "As")
mat = 5.6533 * np.array([0, 1/2, 1/2, 1/2, 0, 1/2, 1/2, 1/2, 0])
mat.shape = (3, 3)
self.assertArrayEqual(inp.structure[1].lattice.matrix, mat)
# tutorial/input/tbase2_1
# 2 datasets with different natom (should use typat[:1] in 2nd dataset)
s = """\
ndtset 2
#Definition of the unit cell and ecut,
#for which one will have to make a convergence study
acell 10 10 10
ecut 10
natom1 2 # There are two atoms
xcart1 -0.7 0.0 0.0 # The starting values of the
0.7 0.0 0.0 # atomic coordinates
#Second dataset : get the total energy of the isolated atom
natom2 1 # There is one atom
xcart2 0.0 0.0 0.0 # The atom is located at the origin
#Definition of the atom types
ntypat 1 # There is only one type of atom
znucl 1 # The keyword "znucl" refers to the atomic number of the
#Definition of the atoms
typat 1 1 # For the first dataset, both numbers will be read,
# while for the second dataset, only one number will be read
"""
inp = AbinitInputFile.from_string(s)
assert inp.ndtset == 2 and inp.structure is None
assert len(inp.datasets[0].structure) == 2
assert len(inp.datasets[1].structure) == 1
str(inp)
def test_enforce_znucl_and_typat(self):
"""Test the order of typat and znucl in the Abinit input when enforce_typat, enforce_znucl are used."""
# Ga Ga1 1 0.33333333333333 0.666666666666667 0.500880 1.0
# Ga Ga2 1 0.66666666666667 0.333333333333333 0.000880 1.0
# N N3 1 0.333333333333333 0.666666666666667 0.124120 1.0
# N N4 1 0.666666666666667 0.333333333333333 0.624120 1.0
gan2 = Structure.from_file(abidata.cif_file("gan2.cif"))
pseudos = abidata.pseudos("31ga.pspnc", "7n.pspnc")
def_znucl = [31, 7]
def_typat = [1, 1, 2, 2]
# Build AbinitInput with default sorting algorithm for znucl and typat
def_inp = AbinitInput(gan2, pseudos)
def_dict = def_inp.as_dict()
assert def_dict["enforce_znucl"] is None
assert def_dict["enforce_typat"] is None
# Build AbinitInput with specific znucl and typat.
enforce_znucl = [7 ,31]
enforce_typat = [2, 2, 1, 1]
enf_inp = AbinitInput(gan2, pseudos, enforce_znucl=enforce_znucl, enforce_typat=enforce_typat)
enf_dict = enf_inp.as_dict()
self.assert_equal(enf_dict["enforce_znucl"], enforce_znucl)
self.assert_equal(enf_dict["enforce_typat"], enforce_typat)
# Parser the input string and make sure znucl and typat are what we expect.
from abipy.abio.abivars import AbinitInputFile
def_string = def_inp.to_string()
enf_string = enf_inp.to_string()
#print("\ndef_string\n", def_string, "\nenf_string:\n", enf_string)
assert def_string != enf_string
def_inpfile = AbinitInputFile.from_string(def_string)
enf_inpfile = AbinitInputFile.from_string(enf_string)
assert def_inpfile.structure == enf_inpfile.structure
self.assert_equal(def_inpfile.datasets[0]["znucl"], " ".join(str(e) for e in def_znucl))
self.assert_equal(def_inpfile.datasets[0]["typat"], " ".join(str(t) for t in def_typat))
self.assert_equal(enf_inpfile.datasets[0]["znucl"], " ".join(str(e) for e in enforce_znucl))
self.assert_equal(enf_inpfile.datasets[0]["typat"], " ".join(str(t) for t in enforce_typat))
other_enf_dict = AbinitInput.from_dict(enf_dict).as_dict()
self.assert_equal(other_enf_dict["enforce_znucl"], enforce_znucl)
self.assert_equal(other_enf_dict["enforce_typat"], enforce_typat)
# Make sure we detect wrong calls.
with self.assertRaises(ValueError):
AbinitInput(gan2, pseudos, enforce_znucl=[1,], enforce_typat=enforce_typat)
with self.assertRaises(ValueError):
AbinitInput(gan2, pseudos, enforce_znucl=enforce_znucl, enforce_typat=[1, 2])
# Make sure enforce flags are propagated in MultiDataset and other methods.
inputs = enf_inp.product("ngkpt", "tsmear", [[2, 2, 2], [4, 4, 4]], [0.1, 0.2, 0.3])
for inp in inputs:
self.assert_equal(inp.enforce_znucl, enforce_znucl)
self.assert_equal(inp.enforce_typat, enforce_typat)
multi = MultiDataset.from_inputs(inputs)
for znucl in multi.enforce_znucl:
self.assert_equal(znucl, enforce_znucl)
for typat in multi.enforce_typat:
self.assert_equal(typat, enforce_typat)