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Merged
vanderhe merged 1 commit into from
Jan 5, 2025
Merged

Rework hybrid extra tag in SK-files #107

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64 changes: 59 additions & 5 deletions sktools/src/sktools/oldskfile.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""Contains the representation of the old SK-file."""


import re
import os.path
import warnings
import numpy as np
Expand Down Expand Up @@ -30,6 +31,12 @@
"""

FLOAT_FORMSTR = " {:20.12E}"
PATTERN_EXTRATAG = (
r"(?i)\s*RangeSep\s*CAM\s+([-+]?(?:[0-9]+\.[0-9]+|\.[0-9]+|[0-9]+)"
r"(?:[eE][-+]?[0-9]+)?)\s+([-+]?(?:[0-9]+\.[0-9]+|\.[0-9]+|[0-9]+)"
r"(?:[eE][-+]?[0-9]+)?)\s+([-+]?(?:[0-9]+\.[0-9]+|\.[0-9]+|[0-9]+)"
r"(?:[eE][-+]?[0-9]+)?)\s*(?:\n|$)"
)


class OldSKFile:
Expand Down Expand Up @@ -85,11 +92,16 @@ def fromfile(cls, fname, homo):
values = sc.convert_fortran_floats(fp.readline())
hamiltonian[iline, 0:ninteg] = values[0:ninteg]
overlap[iline, 0:ninteg] = values[ninteg:2*ninteg]
# Currently, everything after SK table is treated as spline repulsive
splinerep = fp.read()

# the remaining content may contain the spline repulsive and hybrid
# functional tag
remaining_content = fp.read()
splinerep, cam_params = parse_cam_from_content(remaining_content)
extra_tag = generate_cam_extratag(cam_params)

fp.close()
return cls(extended, dr, hamiltonian, overlap, onsites, spinpolerror,
hubbardus, occupations, mass, splinerep, polyrep)
hubbardus, occupations, mass, splinerep, polyrep, extra_tag)


def tofile(self, fname):
Expand Down Expand Up @@ -209,8 +221,21 @@ def equals(self, ref, atol=1e-10, rtol=1e-09):
warnings.warn('Mismatch in nuclear mass.')
return False

# Spline/polynomial repulsive comparison and
# Hyb/LC/CAM tag still missing in comparison
# Spline/polynomial repulsive is still missing in the comparison

if self.extratag and ref.extratag:
_, cam_params_self = parse_cam_from_content(
'\n'.join(self.extratag))
_, cam_params_ref = parse_cam_from_content(
'\n'.join(ref.extratag))
equal = np.allclose(
cam_params_self, cam_params_ref, rtol=rtol, atol=atol)
else:
equal = self.extratag == ref.extratag

if not equal:
warnings.warn('Mismatch in the hybrid functional extra tag.')
return False

return equal

Expand Down Expand Up @@ -467,3 +492,32 @@ def _get_grid_parameters(grid):
def _get_basis_indexed_dict(basis, values):
mydict = {shell: value for shell, value in zip(basis, values)}
return mydict


def parse_cam_from_content(content):
'''Attemps to parse the CAM parameters.'''

match = re.search(PATTERN_EXTRATAG, content)

if match:
cam_params = tuple(map(float, match.groups()))
remaining_content = content[:match.start()] + '\n' \
+ content[match.end():]
else:
cam_params = None
remaining_content = content
remaining_content.strip('\n')

return remaining_content, cam_params


def generate_cam_extratag(cam_params):
'''Generates the extra hybrid functional tag from CAM parameters.'''

if cam_params is not None:
hyb_tag = "RangeSep\nCAM" + 3 * FLOAT_FORMSTR
extra_tag = [hyb_tag.format(*cam_params)]
else:
extra_tag = None

return extra_tag
24 changes: 7 additions & 17 deletions sktools/src/sktools/skgen/sktable.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
import logging
import numpy as np
import sktools.oldskfile
import sktools.common as sc
from .atom import run_atom
from .twocnt import run_twocnt
from sktools.oldskfile import OldSKFileSet, generate_cam_extratag

logger = logging.getLogger("skgen.sktable")

Expand Down Expand Up @@ -150,33 +150,23 @@ def write_sktables(self, workdir, add_dummy_repulsive):
# if range-separated hybrid is used, add the RangeSep tag
extra_tag = None
xcn = myinput.xcf.type
if xcn in ('lcy-bnl', 'lcy-pbe'):
rsh_tag = "RangeSep\nLC {:f}".format(myinput.xcf.omega)
extra_tag = [rsh_tag]
if xcn in ('camy-b3lyp', 'camy-pbeh'):
rsh_tag = "RangeSep\nCAM {:f} {:f} {:f}".format(myinput.xcf.omega,
myinput.xcf.alpha,
myinput.xcf.beta)
extra_tag = [rsh_tag]
if xcn == 'pbe0':
rsh_tag = "GlobalHybrid\nHF {:f}".format(myinput.xcf.alpha)
extra_tag = [rsh_tag]
if xcn == 'b3lyp':
rsh_tag = "GlobalHybrid\nHF {:f}".format(0.20)
extra_tag = [rsh_tag]
if xcn in ('camy-b3lyp', 'camy-pbeh', 'lcy-bnl', 'lcy-pbe', 'pbe0',
'b3lyp'):
extra_tag = generate_cam_extratag((
myinput.xcf.omega, myinput.xcf.alpha, myinput.xcf.beta))

if self._input.homo:
onsites, occs, hubbus, spinpolerr, mass = self._get_atomic_data()
if not myinput.shellresolved:
hubbus = self._override_with_homo_value(
myinput.atomconfig1, self._atom_prereq1.result, hubbus)
skfiles = sktools.oldskfile.OldSKFileSet(
skfiles = OldSKFileSet(
grid, ham, over, valshells1, None, onsites=onsites,
spinpolerror=spinpolerr, hubbardus=hubbus, occupations=occs,
mass=mass, dummy_repulsive=add_dummy_repulsive,
extraTag=extra_tag)
else:
skfiles = sktools.oldskfile.OldSKFileSet(
skfiles = OldSKFileSet(
grid, ham, over, valshells1, valshells2,
dummy_repulsive=add_dummy_repulsive, extraTag=extra_tag)
files_written = skfiles.tofile(workdir, myinput.elem1, myinput.elem2)
Expand Down
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-B3LYP/Non-Relativistic/_C-C.skf
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Expand Up @@ -18,5 +18,5 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.256022427012E-01 -8.967174779220E-02 0.000000000000E+00 2.588766187769E-01 -2.476068796923E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.913955665282E-01 1.068825730890E-01 0.000000000000E+00 -2.603110292313E-01 2.012563001197E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.995367491746E-01 -7.074382263751E-02 0.000000000000E+00 2.198979996171E-01 -2.030911129267E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.604327068317E-01 8.294384940632E-02 0.000000000000E+00 -2.196433484780E-01 1.627465065248E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.746803540072E-01 -5.555299457765E-02 0.000000000000E+00 1.848103257182E-01 -1.649224912594E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.279617062602E-01 6.369812052725E-02 0.000000000000E+00 -1.823952426473E-01 1.298037352539E-01
GlobalHybrid
HF 0.200000
RangeSep
CAM 1.000000 0.200000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-B3LYP/Non-Relativistic/_C-N.skf
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Expand Up @@ -17,5 +17,5 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.385327719867E-01 -8.376675363321E-02 0.000000000000E+00 2.389171365525E-01 -2.382732485867E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.516690162904E-01 8.171730271037E-02 0.000000000000E+00 -2.030862709810E-01 1.612183087232E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.057682402167E-01 -6.462623335249E-02 0.000000000000E+00 1.984604158449E-01 -1.901729152563E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.186341862813E-01 6.191133087953E-02 0.000000000000E+00 -1.674676887709E-01 1.268456159208E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.756483328669E-01 -4.959767584353E-02 0.000000000000E+00 1.630342828745E-01 -1.502026908944E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.861934530822E-01 4.636971032291E-02 0.000000000000E+00 -1.357552608558E-01 9.829733669489E-02
GlobalHybrid
HF 0.200000
RangeSep
CAM 1.000000 0.200000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-B3LYP/Non-Relativistic/_N-C.skf
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Expand Up @@ -17,5 +17,5 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.385327719867E-01 -8.376675363321E-02 0.000000000000E+00 2.840347432011E-01 -2.382732485867E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.516690162904E-01 8.171730271037E-02 0.000000000000E+00 -2.293781587194E-01 1.612183087232E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.057682402167E-01 -6.462623335249E-02 0.000000000000E+00 2.341397683067E-01 -1.901729152563E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.186341862813E-01 6.191133087953E-02 0.000000000000E+00 -1.878686339086E-01 1.268456159208E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.756483328669E-01 -4.959767584353E-02 0.000000000000E+00 1.909765669556E-01 -1.502026908944E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.861934530822E-01 4.636971032291E-02 0.000000000000E+00 -1.514084797748E-01 9.829733669489E-02
GlobalHybrid
HF 0.200000
RangeSep
CAM 1.000000 0.200000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-B3LYP/Non-Relativistic/_N-N.skf
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Expand Up @@ -18,5 +18,5 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.398534554916E-01 -7.422262637971E-02 0.000000000000E+00 2.475351290484E-01 -2.140419370030E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -2.152088904773E-01 6.154360459691E-02 0.000000000000E+00 -1.756356470075E-01 1.248197230168E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2.010969347871E-01 -5.580074594826E-02 0.000000000000E+00 1.987851838413E-01 -1.655244073453E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.812238646371E-01 4.531820634133E-02 0.000000000000E+00 -1.399129083938E-01 9.493842597522E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.668348208848E-01 -4.170162975821E-02 0.000000000000E+00 1.578712051191E-01 -1.265853940311E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.497058014860E-01 3.293389905912E-02 0.000000000000E+00 -1.095037371491E-01 7.096486230961E-02
GlobalHybrid
HF 0.200000
RangeSep
CAM 1.000000 0.200000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-PBE0/Non-Relativistic/_C-C.skf
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Expand Up @@ -21,5 +21,5 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.613294772596E-01 -4.676308320680E-02 0.000000000000E+00 1.697262952307E-01 -1.478961068187E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.996592656583E-01 4.937145659831E-02 0.000000000000E+00 -1.501972432585E-01 1.004955673901E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.388709861288E-01 -3.639137385829E-02 0.000000000000E+00 1.398398998143E-01 -1.176394850715E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.687812602656E-01 3.708664228157E-02 0.000000000000E+00 -1.208696562484E-01 7.773242742221E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.183023070816E-01 -2.813674356221E-02 0.000000000000E+00 1.140529806705E-01 -9.267114153932E-02 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.404149446948E-01 2.751410703501E-02 0.000000000000E+00 -9.579554169696E-02 5.925284604508E-02
GlobalHybrid
HF 0.350000
RangeSep
CAM 1.000000 0.350000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-PBE0/Non-Relativistic/_C-N.skf
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Expand Up @@ -20,5 +20,5 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.598086106448E-01 -4.121621029300E-02 0.000000000000E+00 1.465917121807E-01 -1.299610761722E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.581290422648E-01 3.480034358371E-02 0.000000000000E+00 -1.083088102806E-01 7.353197336217E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.339989808670E-01 -3.131421264213E-02 0.000000000000E+00 1.179363995278E-01 -1.004350517675E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.300584791213E-01 2.539852607010E-02 0.000000000000E+00 -8.477797739917E-02 5.502245996291E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.111818467423E-01 -2.362107213395E-02 0.000000000000E+00 9.387677083199E-02 -7.680800987833E-02 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.052472142457E-01 1.825996663003E-02 0.000000000000E+00 -6.522035385369E-02 4.046850782221E-02
GlobalHybrid
HF 0.350000
RangeSep
CAM 1.000000 0.350000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-PBE0/Non-Relativistic/_N-C.skf
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0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.598086106448E-01 -4.121621029300E-02 0.000000000000E+00 1.694817234966E-01 -1.299610761722E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.581290422648E-01 3.480034358371E-02 0.000000000000E+00 -1.206704112631E-01 7.353197336217E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.339989808670E-01 -3.131421264213E-02 0.000000000000E+00 1.354701908883E-01 -1.004350517675E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.300584791213E-01 2.539852607010E-02 0.000000000000E+00 -9.408171312909E-02 5.502245996291E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.111818467423E-01 -2.362107213395E-02 0.000000000000E+00 1.071346785653E-01 -7.680800987833E-02 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.052472142457E-01 1.825996663003E-02 0.000000000000E+00 -7.212712127355E-02 4.046850782221E-02
GlobalHybrid
HF 0.350000
RangeSep
CAM 1.000000 0.350000 0.000000
4 changes: 2 additions & 2 deletions test/prog/sktable/HYB-PBE0/Non-Relativistic/_N-N.skf
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0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.484665909590E-01 -3.397110940153E-02 0.000000000000E+00 1.366608109025E-01 -1.055516608917E-01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.227547013722E-01 2.375771620947E-02 0.000000000000E+00 -8.395558850122E-02 5.078817991652E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 1.209103581738E-01 -2.510220854089E-02 0.000000000000E+00 1.062285028097E-01 -7.886320157188E-02 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -9.786072787960E-02 1.671819390588E-02 0.000000000000E+00 -6.322003113303E-02 3.638309998039E-02
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 9.742748840751E-02 -1.839742419209E-02 0.000000000000E+00 8.162721617047E-02 -5.823775769877E-02 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -7.669650026162E-02 1.153359045484E-02 0.000000000000E+00 -4.664177240158E-02 2.548739158560E-02
GlobalHybrid
HF 0.350000
RangeSep
CAM 1.000000 0.350000 0.000000
2 changes: 1 addition & 1 deletion test/prog/sktable/LCY-BNL/Non-Relativistic/_N-N.skf
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Expand Up @@ -9,4 +9,4 @@
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 4.251128112329E-01 -8.520413954364E-01 0.000000000000E+00 7.911999264484E-01 -1.195864390877E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -3.125096105836E-02 5.507579595291E-01 0.000000000000E+00 -4.572199054495E-01 6.584063067956E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 5.152677060754E-01 -6.626728103672E-01 0.000000000000E+00 8.204507747816E-01 -1.093677310375E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.665957985938E-01 4.574425782434E-01 0.000000000000E+00 -4.756879621483E-01 5.908017833195E-01
RangeSep
LC 0.300000
CAM 0.300000 0.000000 1.000000
2 changes: 1 addition & 1 deletion test/prog/sktable/LCY-BNL/Non-Relativistic/_N-O.skf
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0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 5.184644474242E-01 -8.842184380269E-01 0.000000000000E+00 8.132455312718E-01 -1.307730556539E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -6.067334254614E-02 5.243983856324E-01 0.000000000000E+00 -4.303815329762E-01 6.412414224181E-01
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 5.891521554104E-01 -6.782716326747E-01 0.000000000000E+00 8.367585632860E-01 -1.172628897477E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -1.858388087924E-01 4.313506531119E-01 0.000000000000E+00 -4.472553760571E-01 5.697366237013E-01
RangeSep
LC 0.300000
CAM 0.300000 0.000000 1.000000
2 changes: 1 addition & 1 deletion test/prog/sktable/LCY-BNL/Non-Relativistic/_O-N.skf
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2 changes: 1 addition & 1 deletion test/prog/sktable/LCY-BNL/Non-Relativistic/_O-O.skf
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RangeSep
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