def test_validate_parameters():
assert validate_parameters({})
assert validate_parameters(get_define_template("dscf"))
assert validate_parameters(get_define_template("ridft"))
assert validate_parameters(get_define_template("dscf_escf"))
assert validate_parameters(get_define_template("ridft_escf"))
assert validate_parameters(get_define_template("ridft_rimp2"))
assert not validate_parameters({"fake_key": 1})
# check dependency
d = {"use_f12*": True}
assert not validate_parameters(d)
d["use_f12"] = True
assert not validate_parameters(d)
d["method"] = "mp2"
assert validate_parameters(d)
#wrong type
assert not validate_parameters({"method": 1})
assert validate_parameters({"disp": "DFT-D1"})
# value not in possible options
assert not validate_parameters({"disp": "wrong_value"})
def test_get_define_template():
"""Testing get define template util function."""
dscf_dict = get_define_template("dscf")
assert dscf_dict["basis"] == "def-SV(P)"
with pytest.raises(ValueError,
match=r'^Could not find template file '
r'\S*non_existing_template.yaml$'):
get_define_template("non_existing_template.yaml")
def test_wrong_method(self, molecule_filepath, delete_tmp_dir):
define_opt = get_define_template("dscf")
define_opt["method"] = "wrong_method"
with temp_dir(delete_tmp_dir) as tmp_dir:
with pytest.raises(DefineParameterError):
self.run_define_runner(define_opt, molecule_filepath)
def test_wrong_xc_func(self, molecule_filepath, delete_tmp_dir):
define_opt = get_define_template("dscf")
define_opt["functional"] = "pbexxxx"
with temp_dir(delete_tmp_dir) as tmp_dir:
with pytest.raises(DefineParameterError):
self.run_define_runner(define_opt, molecule_filepath)
def test_not_converged_ired(self, molecule_filepath, delete_tmp_dir):
define_opt = get_define_template("dscf")
define_opt["ired"] = True
with temp_dir(delete_tmp_dir) as tmp_dir:
with pytest.raises(DefineIredError):
self.run_define_runner(define_opt, molecule_filepath)
def test_run_ridft_aoforce_nosym(self, structure):
dp = get_define_template("ridft")
dp["desy"] = False
assert run_itest(["ridft", "aoforce"], dp, structure,
"ridft_aoforce_{}_nosym".format(structure),
[ScfOutput, AoforceOutput])
def test_run_dscf_aoforce_sym(self, structure):
dp = get_define_template("dscf")
dp["desy"] = True
assert run_itest(["dscf", "aoforce"], dp, structure,
"dscf_aoforce_{}_sym".format(structure),
[ScfOutput, AoforceOutput])
def test_remove_last_energy(self, molecule_filepath, delete_tmp_dir):
"""
Tests the remove_last_energy method of Control.
First runs twice an energy-grad-relax loop, then removes the last
energy and runs escf. The output of escf contains the gs energy and
it reads it from the energy file. The test checks that the value from
the escf.log output corresponds to the first value of the energy and not
to the one that should have been removed.
"""
with temp_dir(delete_tmp_dir) as tmp_dir:
dp = get_define_template("ridft_escf")
run_define_runner(define_opt=dp, mol_path=molecule_filepath)
for i in range(2):
run_tm("ridft")
run_tm("rdgrad")
run_tm("statpt")
c = Control.from_file()
en = c.energy.total
assert len(c.energy.total) == 2
c.remove_last_energy()
run_tm("escf")
p = Parser.from_file("escf.log")
gs_en_from_escf = p.escf_gs_total_en
assert gs_en_from_escf == pytest.approx(en[0])
assert not gs_en_from_escf == pytest.approx(en[1])
def test_remove_last_gradient(self, molecule_filepath, delete_tmp_dir):
"""
Tests the remove_last_gradient method of Control.
First runs twice an energy-grad-relax loop, then removes the last
energy and runs escf. The output of escf contains the gs energy and
it reads it from the energy file. The test checks that the value from
the escf.log output corresponds to the first value of the energy and not
to the one that should have been removed.
"""
with temp_dir(delete_tmp_dir) as tmp_dir:
dp = get_define_template("ridft")
run_define_runner(define_opt=dp, mol_path=molecule_filepath)
run_tm("ridft")
run_tm("rdgrad")
run_tm("statpt")
run_tm("ridft")
run_tm("rdgrad")
c = Control.from_file()
g = c.gradient
assert len(g.gradients) == 2
c.remove_last_gradient()
run_tm("statpt")
p = Parser.from_file("statpt.log")
g_from_statp = p.relax_gradient_values
assert np.allclose(g.norms[0], g_from_statp["norm_cartesian"])
assert not np.allclose(g.norms[1], g_from_statp["norm_cartesian"])
def test_run_ridft_escf(self, structure):
dp = get_define_template("ridft_escf")
dp["desy"] = True
dp["ex_all_states"] = 12
assert run_itest(["ridft", "escf"], dp,
structure, "ridft_escf_{}_std".format(structure), [ScfOutput, EscfOutput])
def test_generate_mo(self, molecule_filepath, delete_tmp_dir):
define_opt = get_define_template("dscf")
with temp_dir(delete_tmp_dir) as tmp:
# run the full to generate all the files
self.run_define_runner(define_opt, molecule_filepath)
os.remove("mos")
self.run_define_runner({}, None, "mo")
assert os.path.isfile("mos")
def test_run_dscf_egrad_relax(self, structure):
dp = get_define_template("dscf_escf")
dp["desy"] = False
dp["ired"] = False
assert run_itest(["dscf", "egrad", "relax"], dp, structure,
"dscf_escf_relax_{}_nosym".format(structure),
[ScfOutput, EgradOutput, RelaxOutput])
def test_run_ridft_rdgrad_relax(self, structure):
dp = get_define_template("ridft")
dp["desy"] = True
dp["ired"] = True
assert run_itest(["ridft", "rdgrad", "relax"], dp, structure,
"ridft_rdgrad_relax_{}_sym".format(structure),
[ScfOutput, GradOutput, StatptOutput])
def test_run_dscf_grad_statpt(self, structure):
dp = get_define_template("dscf")
dp["desy"] = True
dp["ired"] = True
assert run_itest(["dscf", "grad", "statpt"], dp, structure,
"dscf_grad_statpt_{}_sym".format(structure),
[ScfOutput, GradOutput, StatptOutput])
def test_run_ridft_fermi(self, structure):
define_opt = get_define_template("ridft")
define_opt["ri"] = False
define_opt["rijk"] = True
datagroups_options = {"fermi": "tmstrt=500 tmend=50 tmfac=0.9 hlcrt=0.2"}
assert run_itest("ridft", define_opt, structure, "ridft_{}_fermi".format(structure), ScfOutput,
datagroups_options=datagroups_options)
def test_run_ridft_f12x(self, structure):
define_opt = get_define_template("ridft_rimp2")
define_opt["use_f12"] = False
define_opt["use_f12*"] = True
assert run_itest(["ridft", "rimp2"], define_opt, structure,
"ridft_rimp2_{}_f12*".format(structure), {})
def test_run_dscf_escf_charged(self, structure):
dp = get_define_template("dscf_escf")
dp["desy"] = True
dp["ex_all_states"] = 10
dp["charge"] = 1
assert run_itest(["dscf", "escf"], dp,
structure, "dscf_escf_{}_charged".format(structure), [ScfOutput, EscfOutput])
def test_run_dscf_escf(self, structure):
dp = get_define_template("dscf_escf")
dp["desy"] = False
dp["ex_all_states"] = None
dp["ex_irrep_states"] = {"a": 8}
assert run_itest(["dscf", "escf"], dp,
structure, "dscf_escf_{}_std".format(structure), [ScfOutput, EscfOutput])
def test_run_dscf_escf_triplet(self, structure):
dp = get_define_template("dscf_escf")
dp["desy"] = True
dp["ex_all_states"] = 10
dp["ex_multi"] = "triplet"
assert run_itest(["dscf", "escf"], dp,
structure, "dscf_escf_{}_triplet".format(structure), [ScfOutput, EscfOutput])
def test_run_ridft_adc2(self):
define_opt = get_define_template("ridft_rimp2")
define_opt["method"] = "adc(2)"
define_opt["ex_mp2"] = {"a1": [1, 10], "a2": [3, 10]}
define_opt["maxiter"] = 100
define_opt["maxcor"] = 400
assert run_itest(["ridft", "rimp2"], define_opt, "nh3", "ridft_rimp2_nh3_adc2", [ScfOutput, None])
def test_run_ridft_egrad_statpt_ex_irrep(self, structure):
dp = get_define_template("ridft_escf")
dp["desy"] = True
dp["ired"] = True
dp["ex_all_states"] = None
dp["ex_irrep_states"] = {"a1": 1}
assert run_itest(["ridft", "egrad", "statpt"], dp, structure,
"ridft_egrad_statpt_{}_ex_irrep".format(structure),
[ScfOutput, EgradOutput, RelaxOutput])
def test_timeout(self, molecule_filepath, delete_tmp_dir):
"""
Tests an example where expect fails and a DefineExpectError is raised because of TIMEOUT.
"""
define_opt = get_define_template("dscf")
define_opt["scfconv"] = 1e-5
with temp_dir(delete_tmp_dir) as tmp_dir:
with pytest.raises(DefineExpectError):
self.run_define_runner(define_opt, molecule_filepath)
def test_run_jobex_dscf(self, structure):
dp = get_define_template("dscf")
dp["desy"] = True
dp["ired"] = True
assert run_itest("jobex",
dp,
structure,
"jobex_dscf_{}_sym".format(structure),
JobexOutput,
arguments="-c 2")
def test_run_dscf_copymo(self):
"""
Tests the copy functionalities with mos file
"""
define_opt = get_define_template("dscf")
define_opt["basis"] = "def2-SV(P)"
define_opt["copymo"] = os.path.join(get_tfp(), "mo", "mos_nh3")
assert run_itest("dscf", define_opt, "nh3", "dscf_nh3_copymo_mos",
ScfOutput)
def test_eof(self, molecule_filepath, delete_tmp_dir):
"""
Tests an example where expect fails and a DefineExpectError is raised because of EOF.
"""
define_opt = get_define_template("ridft_rimp2")
define_opt["method"] = "ccsdt"
define_opt["mp2energy"] = False
with temp_dir(delete_tmp_dir) as tmp_dir:
with pytest.raises(DefineExpectError):
self.run_define_runner(define_opt, molecule_filepath)
def test_run_dscf_hf(self, structure):
define_opt = get_define_template("dscf")
define_opt["method"] = "hf"
define_opt["desy"] = False
define_opt["sym"] = "c1"
define_opt["sym_eps"] = 0.001
define_opt["scfiterlimit"] = 300
define_opt["scfconv"] = 6
define_opt["title"] = None
assert run_itest("dscf", define_opt, structure,
"dscf_{}_hf".format(structure), ScfOutput)
def test_run_dscf_copymo_alpha_unpaired(self):
"""
Tests the copy functionalities with mos file
"""
define_opt = get_define_template("dscf")
define_opt["basis"] = "def2-SV(P)"
define_opt["charge"] = 1
define_opt["unpaired_electrons"] = 1
define_opt["copymo"] = os.path.join(get_tfp(), "mo", "alpha_beta_nh3")
assert run_itest("dscf", define_opt, "nh3",
"dscf_nh3_copymo_alpha_unpaired", ScfOutput)
def test_generate_mo_symmetry(self, molecule_filepath, delete_tmp_dir):
define_opt = get_define_template("dscf")
define_opt["desy"] = True
with temp_dir(delete_tmp_dir) as tmp:
# run the full to generate all the files
self.run_define_runner(define_opt, molecule_filepath)
s = States.from_file("control")
# check that there are other irreps coming from the mos
assert len(s.irreps) != 1 or s.irreps[0] != "a"
# do not remove mos to trigger another path in DefineRunner
self.run_define_runner({"sym": "c1"}, None, "mo")
assert os.path.isfile("mos")
s_new = States.from_file("control")
assert s_new.irreps[0] == "a"
def testrun_update_internal_coords(self, molecule_filepath,
delete_tmp_dir):
define_opt = get_define_template("dscf")
define_opt["ired"] = True
with temp_dir(delete_tmp_dir) as tmp:
# run the full to generate all the files
self.run_define_runner(define_opt, molecule_filepath)
s = States.from_file("control")
dg = DataGroups.from_file("coord")
dg.kdg("redundant")
dg.to_file("coord")
# do not remove mos to trigger another path in DefineRunner
self.run_define_runner({"ired": True}, None, "internal")
dg_new = DataGroups.from_file("coord")
assert dg_new.sdg("redundant")
def test_run_dscf_cosmo(self, structure):
define_opt = get_define_template("dscf")
define_opt["use_cosmo"] = True
define_opt.update({
"epsilon": 60.0,
"nppa": 92,
"nspa": None,
"disex": 0,
"rsolv": 1.3,
"routf": None,
"cavity": "open"
})
assert run_itest("dscf", define_opt, structure,
"dscf_{}_cosmo".format(structure), ScfOutput)
