def test_condition_number():
with open(TEST_DIR.joinpath("inputs/overlap_condition_snippet.out"),
"r") as fhandle:
result = next(
parse_iter(fhandle.read(),
matchers=[match_overlap_matrix_condition_number]))
assert result
assert result == {
"overlap_matrix_condition_number": {
"1-norm (estimate)": {
"|A|": 15.13,
"|A^-1|": 7525.0,
"CN": 113900.0,
"Log(CN)": 5.0563
},
"1-norm (using diagonalization)": {
"|A|": 15.13,
"|A^-1|": 22980.0,
"CN": 347700.0,
"Log(CN)": 5.5412
},
"2-norm (using diagonalization)": {
"max EV": 10.81,
"min EV": 0.0001036,
"CN": 104400.0,
"Log(CN)": 5.0187
},
}
}
def test_mulliken_unrestricted():
with open(TEST_DIR.joinpath("inputs/mulliken_unrestricted_snippet.out"), "r") as fhandle:
result = next(parse_iter(fhandle.read(), matchers=[match_mulliken_population_analysis]))
assert result
assert result == {
"mulliken population analysis": {
"per atom": [
{
"element": "Co",
"kind": 1,
"population alpha": 9.332183,
"population beta": 7.66782,
"charge": -2e-06,
"spin": 1.664363,
},
{
"element": "Co",
"kind": 1,
"population alpha": 9.332177,
"population beta": 7.66782,
"charge": 2e-06,
"spin": 1.664357,
},
],
"total": {"population alpha": 18.66436, "population beta": 15.33564, "charge": -0.0, "spin": 3.32872},
}
}
def test_energies():
with open(TEST_DIR.joinpath("inputs/Si.out"), "r") as fhandle:
result = next(parse_iter(fhandle.read(), matchers=[match_energies]))
assert result
assert result == {
"energies": {
"total force_eval": -251.687390311050706
}
}
def test_no_stop():
with open(TEST_DIR.joinpath("inputs/Si-truncated.out"), "r") as fhandle:
result = next(parse_iter(fhandle.read(), matchers=[match_program_info]))
assert result
assert result == {
"program info": {
"started at": "2019-09-17 17:01:19.273",
"started on": "tcpc18",
"started by": "tiziano",
"process id": "23773",
"started in": "/users/tiziano/work/phonopy/example/Si-CP2K",
}
}
def test_warnings():
with open(TEST_DIR.joinpath("inputs/warning-snippet.out"), "r") as fhandle:
result = next(parse_iter(fhandle.read(), matchers=[match_warnings]))
assert result
assert result == {
"nwarnings": 2,
"warnings": [
{
"filename": "qs_scf_post_gpw.F",
"line": 2162,
"message": "Spin contamination estimate not implemented for k-points.",
}
],
}
def test_kv_sections():
with open(TEST_DIR.joinpath("inputs/Si.out"), "r") as fhandle:
result = next(parse_iter(fhandle.read(), matchers=[match_kv_sections]))
assert result
assert result == {
"cp2k": {
"cp2kflags": "libint fftw3 libxc xsmm spglib",
"data directory path": "/data/tiziano/cp2k/data",
"input file name": "Si-supercell-001.inp",
"is freely available from": "https://www.cp2k.org/",
"program compiled at": "Mon Sep 16 14:42:43 CEST 2019",
"program compiled for": "local",
"program compiled on": "tcpc18",
"source code revision number": "git:43f50e2",
"version string": "CP2K version 7.0 (Development Version)",
},
"dbcsr": {
"cpu multiplication driver": "XSMM",
"maximum elements for images": "UNLIMITED",
"multiplication size stacks": 3,
"multiplication stack size": 1000,
"multiplicative factor virtual images": 1,
"multrec recursion limit": 512,
"use multiplication densification": True,
},
"dft": {
"charge": 0,
"cutoffs": {
"cutoff_smoothing_range": 0.0,
"density": 1e-10,
"gradient": 1e-10,
"tau": 1e-10
},
"multiplicity": 1,
"number of spin states": 1,
"self-interaction correction (sic)": "NO",
"spin restricted kohn-sham (rks) calculation": "RKS",
"xc density smoothing": "NONE",
"xc derivatives": "PW",
},
"global": {
"all-to-all communication in single precision": False,
"basis set file name": "BASIS_MOLOPT",
"coordinate file name": "__STD_INPUT__",
"cpu model name": "Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz",
"cpuid": 1002,
"ffts using library dependent lengths": False,
"force environment number": 1,
"global print level": "MEDIUM",
"method name": "CP2K",
"mm potential file name": "MM_POTENTIAL",
"mpi i/o enabled": True,
"number of threads for this process": 1,
"potential file name": "POTENTIAL",
"preferred diagonalization lib.": "SL",
"preferred fft library": "FFTW3",
"project name": "Si-supercell-001",
"run type": "ENERGY_FORCE",
"this output is from process": 0,
"total number of message passing processes": 1,
},
"qs": {
"density cutoff [a.u.]": 140.0,
"density plane wave grid type": "NON-SPHERICAL FULLSPACE",
"grid level progression factor": 3.0,
"interaction thresholds": {
"eps_core_charge": 1e-12,
"eps_filter_matrix": 0.0,
"eps_gvg_rspace": 1e-05,
"eps_ppl": 0.01,
"eps_ppnl": 1e-07,
"eps_rho_gspace": 1e-10,
"eps_rho_rspace": 1e-10,
"ps_pgf_orb": 1e-05,
},
"method": "GPW",
"multi grid cutoff [a.u.]": {
"1) grid level": 140.0,
"2) grid level": 46.7,
"3) grid level": 15.6,
"4) grid level": 5.2,
},
"number of grid levels": 4,
"relative density cutoff [a.u.]": 20.0,
},
}
def test_parse_safe_keys():
with open(TEST_DIR.joinpath("inputs/Si.out"), "r") as fhandle:
for match in parse_iter(fhandle.read(), key_mangling=True):
assert not any(c in key for c in FORBIDDEN_CHARS
for key in _key_iter(match))
def test_no_start_and_stop():
with open(TEST_DIR.joinpath("inputs/mulliken_restricted_snippet.out"), "r") as fhandle:
with pytest.raises(StopIteration):
next(parse_iter(fhandle.read(), matchers=[match_program_info]))
def test_mulliken_restricted():
with open(TEST_DIR.joinpath("inputs/mulliken_restricted_snippet.out"), "r") as fhandle:
result = next(parse_iter(fhandle.read(), matchers=[match_mulliken_population_analysis]))
assert result
assert result == {
"mulliken population analysis": {
"per atom": [
{"element": "Si", "kind": 1, "population": 3.999993, "charge": 7e-06},
{"element": "Si", "kind": 1, "population": 4.0, "charge": 0.0},
{"element": "Si", "kind": 1, "population": 4.0, "charge": -0.0},
{"element": "Si", "kind": 1, "population": 4.000001, "charge": -1e-06},
{"element": "Si", "kind": 1, "population": 4.0, "charge": -0.0},
{"element": "Si", "kind": 1, "population": 4.000001, "charge": -1e-06},
{"element": "Si", "kind": 1, "population": 4.000001, "charge": -1e-06},
{"element": "Si", "kind": 1, "population": 4.0, "charge": -0.0},
{"element": "Si", "kind": 1, "population": 3.999863, "charge": 0.000137},
{"element": "Si", "kind": 1, "population": 4.00002, "charge": -2e-05},
{"element": "Si", "kind": 1, "population": 4.000133, "charge": -0.000133},
{"element": "Si", "kind": 1, "population": 3.999979, "charge": 2.1e-05},
{"element": "Si", "kind": 1, "population": 4.000133, "charge": -0.000133},
{"element": "Si", "kind": 1, "population": 3.999979, "charge": 2.1e-05},
{"element": "Si", "kind": 1, "population": 3.999863, "charge": 0.000137},
{"element": "Si", "kind": 1, "population": 4.00002, "charge": -2e-05},
{"element": "Si", "kind": 1, "population": 4.000039, "charge": -3.9e-05},
{"element": "Si", "kind": 1, "population": 3.999964, "charge": 3.6e-05},
{"element": "Si", "kind": 1, "population": 4.00001, "charge": -1e-05},
{"element": "Si", "kind": 1, "population": 3.99999, "charge": 1e-05},
{"element": "Si", "kind": 1, "population": 4.000039, "charge": -3.9e-05},
{"element": "Si", "kind": 1, "population": 3.999964, "charge": 3.6e-05},
{"element": "Si", "kind": 1, "population": 4.00001, "charge": -1e-05},
{"element": "Si", "kind": 1, "population": 3.99999, "charge": 1e-05},
{"element": "Si", "kind": 1, "population": 4.000039, "charge": -3.9e-05},
{"element": "Si", "kind": 1, "population": 3.999964, "charge": 3.6e-05},
{"element": "Si", "kind": 1, "population": 4.000039, "charge": -3.9e-05},
{"element": "Si", "kind": 1, "population": 3.999964, "charge": 3.6e-05},
{"element": "Si", "kind": 1, "population": 4.00001, "charge": -1e-05},
{"element": "Si", "kind": 1, "population": 3.99999, "charge": 1e-05},
{"element": "Si", "kind": 1, "population": 4.00001, "charge": -1e-05},
{"element": "Si", "kind": 1, "population": 3.99999, "charge": 1e-05},
{"element": "Si", "kind": 1, "population": 3.999994, "charge": 6e-06},
{"element": "Si", "kind": 1, "population": 3.999965, "charge": 3.5e-05},
{"element": "Si", "kind": 1, "population": 3.999967, "charge": 3.3e-05},
{"element": "Si", "kind": 1, "population": 3.999991, "charge": 9e-06},
{"element": "Si", "kind": 1, "population": 3.999967, "charge": 3.3e-05},
{"element": "Si", "kind": 1, "population": 3.999991, "charge": 9e-06},
{"element": "Si", "kind": 1, "population": 3.999997, "charge": 3e-06},
{"element": "Si", "kind": 1, "population": 4.000312, "charge": -0.000312},
{"element": "Si", "kind": 1, "population": 3.999997, "charge": 3e-06},
{"element": "Si", "kind": 1, "population": 4.000311, "charge": -0.000311},
{"element": "Si", "kind": 1, "population": 3.999966, "charge": 3.4e-05},
{"element": "Si", "kind": 1, "population": 3.99999, "charge": 1e-05},
{"element": "Si", "kind": 1, "population": 3.999966, "charge": 3.4e-05},
{"element": "Si", "kind": 1, "population": 3.99999, "charge": 1e-05},
{"element": "Si", "kind": 1, "population": 3.999994, "charge": 6e-06},
{"element": "Si", "kind": 1, "population": 3.999965, "charge": 3.5e-05},
{"element": "Si", "kind": 1, "population": 4.000009, "charge": -9e-06},
{"element": "Si", "kind": 1, "population": 4.000033, "charge": -3.3e-05},
{"element": "Si", "kind": 1, "population": 3.999692, "charge": 0.000308},
{"element": "Si", "kind": 1, "population": 4.000004, "charge": -4e-06},
{"element": "Si", "kind": 1, "population": 4.000036, "charge": -3.6e-05},
{"element": "Si", "kind": 1, "population": 4.000007, "charge": -7e-06},
{"element": "Si", "kind": 1, "population": 4.000009, "charge": -9e-06},
{"element": "Si", "kind": 1, "population": 4.000033, "charge": -3.3e-05},
{"element": "Si", "kind": 1, "population": 4.000008, "charge": -8e-06},
{"element": "Si", "kind": 1, "population": 4.000033, "charge": -3.3e-05},
{"element": "Si", "kind": 1, "population": 4.000035, "charge": -3.5e-05},
{"element": "Si", "kind": 1, "population": 4.000006, "charge": -6e-06},
{"element": "Si", "kind": 1, "population": 3.999692, "charge": 0.000308},
{"element": "Si", "kind": 1, "population": 4.000004, "charge": -4e-06},
{"element": "Si", "kind": 1, "population": 4.000008, "charge": -8e-06},
{"element": "Si", "kind": 1, "population": 4.000033, "charge": -3.3e-05},
],
"total": {"population": 256.0, "charge": 0.0},
}
}
def test_no_mulliken():
with pytest.raises(StopIteration):
next(parse_iter("", matchers=[match_mulliken_population_analysis]))