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Add energy contributions #36

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13d82b4
Add different energies to energies and inner-scf blocks.
Dec 9, 2023
60efdb4
Adjust tests and change output format for levelparser.
Dec 9, 2023
49b9657
Update cp2k_output_tools/blocks/energies.py
hdsassnick Dec 11, 2023
ede7500
Update cp2k_output_tools/blocks/energies.py
hdsassnick Dec 11, 2023
a055b49
Update cp2k_output_tools/blocks/energies.py
hdsassnick Dec 11, 2023
e74b640
Update cp2k_output_tools/blocks/energies.py
hdsassnick Dec 11, 2023
48e3554
Name INNER_SCF_CONV_RE pattern back to INNER_SCF_END_RE to avoid back…
Dec 11, 2023
3591c12
Reverse nested list for spans.
Dec 11, 2023
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32 changes: 28 additions & 4 deletions cp2k_output_tools/blocks/energies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,23 @@

from .common import FLOAT, BlockMatch

MAIN_ENERGY_RE = re.compile(
rf"""
^\s*Overlap\ energy\ of\ the\ core\ charge\ distribution:\s*(?P<overlap_core>{FLOAT})\n
\s*Self\ energy\ of\ the\ core\ charge\ distribution:\s*(?P<self_core>{FLOAT})\n
\s*Core\ Hamiltonian\ energy:\s*(?P<core_hamiltonian>{FLOAT})\n
\s*Hartree\ energy:\s*(?P<hartree>{FLOAT})\n
(?:\s*Exchange-correlation\ energy:\s*(?P<xc>{FLOAT})\n)?
(?:\s*Electronic\ entropic\ energy:\s*(?P<electronic_entropic>{FLOAT})\n)?
(?:\s*Fermi\ energy:\s*(?P<fermi>{FLOAT})\n)?
(?:\s*Dispersion\ energy:\s*(?P<dispersion>{FLOAT})\n)?
\n
\s*Total\ energy:\s*(?P<total>{FLOAT})\n
""",
re.VERBOSE | re.MULTILINE,
)


FORCE_EVAL_ENERGY_RE = re.compile(
rf"""
^\s*ENERGY\|\ Total\ FORCE_EVAL [^:]+:\s*(?P<value>{FLOAT})\n
Expand All @@ -13,9 +30,16 @@


def match_energies(content: str) -> Optional[BlockMatch]:
spans = []
energies = {}
match = MAIN_ENERGY_RE.search(content)
if match:
energies = match.groupdict()
spans = match.spans(0)
match = FORCE_EVAL_ENERGY_RE.search(content)

if not match:
if match:
energies["total force_eval"] = match["value"]
spans += match.spans(0)
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Suggested change
spans += match.spans(0)
spans += [match.spans(0)]

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I reversed this change since it was resulting in the cli tests to fail. Checking the output I believe that my original implementation was actually already giving the correct output?

if not energies:
return None

return BlockMatch({"energies": {"total force_eval": float(match["value"])}}, match.spans(0))
return BlockMatch({"energies": {key: float(val) for key, val in energies.items() if val is not None}}, spans)
23 changes: 19 additions & 4 deletions cp2k_output_tools/blocks/scf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

from . import UREG
from .common import FLOAT, Level
from .energies import FORCE_EVAL_ENERGY_RE
from .energies import FORCE_EVAL_ENERGY_RE, MAIN_ENERGY_RE
from .mulliken import MULLIKEN_POPULATION_ANALYSIS_RE
from .warnings import Message, match_messages

Expand Down Expand Up @@ -132,6 +132,15 @@ class OuterSCF(Level):
class InnerSCF(Level):
converged: bool
nsteps: int
overlap_core_energy: Decimal
self_core_energy: Decimal
core_hamiltonian_energy: Decimal
hartree_energy: Decimal
xc_energy: Decimal
total_energy: Decimal
electronic_entropic_energy: Optional[Decimal] = None
fermi_energy: Optional[Decimal] = None
dispersion_energy: Optional[Decimal] = None


@dataclass
Expand Down Expand Up @@ -194,11 +203,17 @@ def match_scf(content: str, start: int = 0, end: int = sys.maxsize) -> Optional[
match = INNER_SCF_START_RE.search(content, start, end)
if match:
start = match.span()[1]
ematch = INNER_SCF_END_RE.search(content, start, end)
if ematch:
energy_match = MAIN_ENERGY_RE.search(content, start, end)
conv_match = INNER_SCF_END_RE.search(content, start, end)
if conv_match and energy_match:
start = match.span()[1]
kwargs = {
key + "_energy": Decimal(val) * UREG.hartree for key, val in energy_match.groupdict().items() if val is not None
}
sublevels.append(
InnerSCF(converged="SCF run converged" in ematch["convtxt"], nsteps=int(ematch["nsteps"]), sublevels=[])
InnerSCF(
converged="SCF run converged" in conv_match["convtxt"], nsteps=int(conv_match["nsteps"]), **kwargs, sublevels=[]
)
)

force_eval_energy: Optional[Decimal] = None
Expand Down
14 changes: 13 additions & 1 deletion tests/test_energies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,4 +9,16 @@ def test_energies():
result = next(parse_iter(fhandle.read(), matchers=[match_energies]))

assert result
assert result == {"energies": {"total force_eval": -251.687390311050706}}
assert result == {
"energies": {
"core_hamiltonian": 138.60026809219576,
"electronic_entropic": -1.256404e-08,
"fermi": 0.20382509931778,
"hartree": 343.3040142273272,
"overlap_core": 3.0088e-10,
"self_core": -656.5115154010256,
"total": -251.63989121633358,
"xc": -77.03265812258856,
"total force_eval": -251.687390311050706,
}
}
128 changes: 117 additions & 11 deletions tests/test_optimization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,35 +13,79 @@
"num_occ_orb": 1,
"num_mol_orb": 1,
"num_orb_func": 10,
"nsteps": 8,
"force_eval_energy": -1.16096052,
"inner_scf": {
"nsteps": 8,
"overlap_core_energy": 6.0512959e-07,
"self_core_energy": -2.82094792,
"core_hamiltonian_energy": 1.07883184,
"hartree_energy": 1.30392538,
"xc_energy": -0.72277042,
"total_energy": -1.16096052,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 2,
"num_occ_orb": 1,
"num_mol_orb": 1,
"num_orb_func": 10,
"nsteps": 4,
"force_eval_energy": -1.16118019,
"inner_scf": {
"nsteps": 4,
"overlap_core_energy": 0.0000012,
"self_core_energy": -2.82094792,
"core_hamiltonian_energy": 1.08370608,
"hartree_energy": 1.30183473,
"xc_energy": -0.72577425,
"total_energy": -1.16118019,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 2,
"num_occ_orb": 1,
"num_mol_orb": 1,
"num_orb_func": 10,
"nsteps": 4,
"force_eval_energy": -1.16118537,
"inner_scf": {
"nsteps": 4,
"overlap_core_energy": 1.07320985e-06,
"self_core_energy": -2.82094792,
"core_hamiltonian_energy": 1.08302262,
"hartree_energy": 1.30210002,
"xc_energy": -0.72536117,
"total_energy": -1.16118537,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 2,
"num_occ_orb": 1,
"num_mol_orb": 1,
"num_orb_func": 10,
"nsteps": 4,
"force_eval_energy": -1.16118537,
"inner_scf": {
"nsteps": 4,
"overlap_core_energy": 1.07320985e-06,
"self_core_energy": -2.82094792,
"core_hamiltonian_energy": 1.08302280,
"hartree_energy": 1.30210002,
"xc_energy": -0.72536117,
"total_energy": -1.16118537,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
],
},
Expand All @@ -53,44 +97,99 @@
"num_occ_orb": 16,
"num_mol_orb": 16,
"num_orb_func": 55,
"nsteps": 10,
"force_eval_energy": -65.98706397,
"inner_scf": {
"nsteps": 10,
"overlap_core_energy": 0.0,
"self_core_energy": -138.89582544,
"core_hamiltonian_energy": 27.22305865,
"hartree_energy": 56.70225641,
"xc_energy": -11.01655328,
"total_energy": -65.98706366,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 32,
"num_occ_orb": 16,
"num_mol_orb": 16,
"num_orb_func": 55,
"nsteps": 9,
"force_eval_energy": -65.98706506,
"inner_scf": {
"nsteps": 9,
"overlap_core_energy": 0.0,
"self_core_energy": -138.89582544,
"core_hamiltonian_energy": 27.22275912,
"hartree_energy": 56.70220023,
"xc_energy": -11.01647284,
"total_energy": -65.98733894,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 32,
"num_occ_orb": 16,
"num_mol_orb": 16,
"num_orb_func": 55,
"nsteps": 5,
"force_eval_energy": -65.98710767,
"inner_scf": {
"nsteps": 5,
"overlap_core_energy": 0.0,
"self_core_energy": -138.89582544,
"core_hamiltonian_energy": 27.20749466,
"hartree_energy": 56.71104696,
"xc_energy": -11.00902476,
"total_energy": -65.98630859,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 32,
"num_occ_orb": 16,
"num_mol_orb": 16,
"num_orb_func": 55,
"nsteps": 4,
"force_eval_energy": -65.98710770,
"inner_scf": {
"nsteps": 4,
"overlap_core_energy": 0.0,
"self_core_energy": -138.89582544,
"core_hamiltonian_energy": 27.20670707,
"hartree_energy": 56.71083178,
"xc_energy": -11.00884866,
"total_energy": -65.98713525,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
{
"nspin": 1,
"nelec": 32,
"num_occ_orb": 16,
"num_mol_orb": 16,
"num_orb_func": 55,
"nsteps": 1,
"force_eval_energy": -65.98710770,
"inner_scf": {
"nsteps": 1,
"overlap_core_energy": 0.0,
"self_core_energy": -138.89582544,
"core_hamiltonian_energy": 27.20676302,
"hartree_energy": 56.71080149,
"xc_energy": -11.00884677,
"total_energy": -65.98710770,
"electronic_entropic_energy": None,
"fermi_energy": None,
"dispersion_energy": None,
},
},
],
"cell_infos": [
Expand Down Expand Up @@ -149,12 +248,19 @@ def test_optimization(opt_type):
for step_scf, opt_ref in zip(opt_steps_scf + [result.levels[0].sublevels[1]], ref["opt"]):
assert step_scf.converged
assert step_scf.sublevels[0].converged
inner_scf_ref = opt_ref.pop("inner_scf")
inner_scf = step_scf.sublevels[0]
for keyw, val in inner_scf_ref.items():
if val is None:
assert getattr(inner_scf, keyw) is None
elif isinstance(val, float):
assert abs(float(getattr(inner_scf, keyw).magnitude) - val) < 1.0e-7
else:
assert getattr(inner_scf, keyw) == val
assert abs(float(step_scf.force_eval_energy.magnitude) - opt_ref.pop("force_eval_energy")) < 1.0e-7
assert step_scf.sublevels[0].nsteps == opt_ref.pop("nsteps")
for keyw, val in opt_ref.items():
assert getattr(step_scf, keyw) == val
if opt_type == "cell":
print(result.levels[0].cell_infos)
assert len(result.levels[0].cell_infos) == len(ref["cell_infos"])
for info, ref_info in zip(result.levels[0].cell_infos, ref["cell_infos"]):
assert abs(float(info.volume.magnitude) - ref_info.pop("volume")) < 1.0e-7
Expand Down