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NRL update #57

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merged 5 commits into from
Dec 29, 2023
Merged

NRL update #57

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7eda0dd
update nrl formula to support both the v0 and v1 overlap formula in …
QG-phy Dec 27, 2023
ef06540
update NRL: add a tool to transfer NRL para text file to the json mod…
QG-phy Dec 27, 2023
a3c90d6
update NRL the out ckpt file name
QG-phy Dec 27, 2023
1000f4f
add example of Cu
QG-phy Dec 27, 2023
ce5e61f
update the example of Silicon
QG-phy Dec 27, 2023
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31 changes: 31 additions & 0 deletions dptb/entrypoints/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
from dptb.entrypoints.test import _test
from dptb.entrypoints.run import run
from dptb.entrypoints.bond import bond
from dptb.entrypoints.nrl2json import nrl2json
from dptb.utils.loggers import set_log_handles

def get_ll(log_level: str) -> int:
Expand Down Expand Up @@ -111,6 +112,33 @@ def main_parser() -> argparse.ArgumentParser:
help="The cutoff radius of bond search.",
)

# nrl2json
parser_nrl2json = subparsers.add_parser(
"n2j",
parents=[parser_log],
help="using DeePTB tools to convert NRL file to json model.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser_nrl2json.add_argument(
"INPUT", help="the input parameter file in json or yaml format",
type=str,
default=None
)
parser_nrl2json.add_argument(
"-nrl",
"--nrl_file",
type=str,
default=None,
help="The NRL file name"
)
parser_nrl2json.add_argument(
"-o",
"--outdir",
type=str,
default="./",
help="The output files to save the transfered model and updated input."
)

# train parser
parser_train = subparsers.add_parser(
"train",
Expand Down Expand Up @@ -321,3 +349,6 @@ def main():

elif args.command == 'run':
run(**dict_args)

elif args.command == 'n2j':
nrl2json(**dict_args)
23 changes: 23 additions & 0 deletions dptb/entrypoints/nrl2json.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
from typing import Dict, List, Optional, Any
import ase.io as io
from pathlib import Path
from dptb.utils.read_NRL_tojson import read_nrl_file, nrl2dptb, save2json
import os
import logging
log = logging.getLogger(__name__)

def nrl2json(
INPUT: str,
nrl_file: str,
outdir: str,
log_level: int,
log_path: Optional[str],
**kwargs
):

NRL_data = read_nrl_file(nrl_file)
input_dict, nrl_tb_dict = nrl2dptb(INPUT, NRL_data)
save2json(input_dict, nrl_tb_dict, outdir)
log.info(f'NRL file {nrl_file} has been converted to {outdir}/nrl_ckpt.json.')
log.info(f'INPUT json is updated to {outdir}/input_nrl_auto.json.')
log.info('Please check the json file and modify the parameters if necessary.')
25 changes: 17 additions & 8 deletions dptb/nnsktb/formula.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import torch as th
from abc import ABC, abstractmethod
from dptb.nnsktb.bondlengthDB import bond_length

import re

class BaseSK(ABC):
def __init__(self) -> None:
Expand Down Expand Up @@ -35,15 +35,14 @@ def __init__(self, functype='varTang96',overlap=False) -> None:
self.num_paras = 2
assert hasattr(self, 'powerlaw')

elif functype == 'NRL':
elif re.search("NRL",functype):
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这边原来"=="会出啥问题嘛

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你应该也看到了，我为了兼容两种版本的NRL, 在input json里面指定模式的时候，NRLv0 和NRLv1 两种字段。这样的改成正则的判断是否是NRL就可以兼容这两种。最小变动。

self.functype = functype
self.num_paras = 4
assert hasattr(self, 'NRL_HOP')
if overlap:
self.overlap_num_paras = 4
assert hasattr(self, 'NRL_OVERLAP')


elif functype =='custom':
# the functype custom, is for user to define their own formula.
# just modify custom to the name of your formula.
Expand All @@ -68,7 +67,7 @@ def skhij(self, rij, **kwargs):
return self.varTang96(rij=rij, **kwargs)
elif self.functype == 'powerlaw':
return self.powerlaw(rij=rij, **kwargs)
elif self.functype == 'NRL':
elif re.search("NRL",self.functype):
return self.NRL_HOP(rij=rij, **kwargs)
else:
raise ValueError('No such formula')
Expand All @@ -83,8 +82,13 @@ def sksij(self,rij,**kwargs):
'''
assert self.overlap, 'overlap is False, no overlap function is defined.'

if self.functype == 'NRL':
return self.NRL_OVERLAP(rij=rij, **kwargs)
if self.functype == 'NRLv0':
return self.NRL_OVERLAP(rij=rij,overlap_type=0, **kwargs)
elif self.functype == 'NRLv1':
return self.NRL_OVERLAP(rij=rij,overlap_type=1, **kwargs)
elif self.functype == "NRL":
# default is designed for overlap type 1.
return self.NRL_OVERLAP(rij=rij,overlap_type=1, **kwargs)
else:
raise ValueError('No such formula')

Expand Down Expand Up @@ -146,7 +150,7 @@ def NRL_HOP(self, rij, paraArray, rcut:th.float32 = th.tensor(6), w:th.float32 =

return (a + b * rij + c * rij**2) * th.exp(-d**2 * rij)*f_rij

def NRL_OVERLAP(self, rij, paraArray, paraconst, rcut:th.float32 = th.tensor(6), w:th.float32 = 0.1, **kwargs):
def NRL_OVERLAP(self, rij, paraArray, paraconst, rcut:th.float32 = th.tensor(6), w:th.float32 = 0.1, overlap_type=1, **kwargs):
"""
This function calculates the Overlap value of the form of NRL-TB

Expand Down Expand Up @@ -175,4 +179,9 @@ def NRL_OVERLAP(self, rij, paraArray, paraconst, rcut:th.float32 = th.tensor(6),
f_rij = 1/(1+th.exp((rij-rcut+5*w)/w))
f_rij[rij>=rcut] = 0.0

return (delta_ll + a * rij + b * rij**2 + c * rij**3) * th.exp(-d**2 * rij)*f_rij
if overlap_type==1:
return (delta_ll + a * rij + b * rij**2 + c * rij**3) * th.exp(-d**2 * rij)*f_rij
elif overlap_type ==0:
return (a + b * rij + c * rij**2) * th.exp(-d**2 * rij)*f_rij
else:
raise ValueError('No such overlap type')
4 changes: 2 additions & 2 deletions dptb/nnsktb/integralFunc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
from dptb.nnsktb.formula import SKFormula
from dptb.utils.index_mapping import Index_Mapings
from dptb.nnsktb.skintTypes import all_skint_types, all_onsite_intgrl_types, NRL_skint_type_constants

import re

# define the function for output all the hoppongs for given i,j.

Expand All @@ -20,7 +20,7 @@ def __init__(self, proj_atom_anglr_m, atomtype=None, mode='hopping', functype='v
self.bond_index_dict = sk_bond_ind_dict
self.para_Consts = None

if functype == 'NRL':
if re.search("NRL",functype):
self.para_Consts = NRL_skint_type_constants(reducted_skint_types)
# call to get the para constants!
# special onsite mode for strain, which use same sk strategy as hopping.
Expand Down
104 changes: 104 additions & 0 deletions dptb/tests/data/nrl/Cu.par
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Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
NN00000 (Old style Overlap Parameters)
Copper (Cu)
1 (One atom type in this file)
16.5 0.5 (RCUT and SCREENL for 1-1 interactions)
9 (Orbitals for atom 1)
63.54 (Atomic Weight of Atom 1)
1.0 0.0 10.0 (formal spd valence occupancy for atom 1)
1.47291793797E+00 0 1 lambda (equation 7)
2.13397883099E-02 0 2 a_s (equation 9)
6.93938937933E+01 0 3 b_s (equation 9)
-2.44786970765E+03 0 4 c_s (equation 9)
0.00000000000E+00 1 5 d_s (equation 9)
5.55994187020E-01 0 6 a_p (equation 9)
4.82151716250E+01 0 7 b_p (equation 9)
-3.82848296416E+02 0 8 c_p (equation 9)
0.00000000000E+00 1 9 d_p (equation 9)
1.99140354046E-02 0 10 a_t2g (equation 9)
3.46551434776E-01 0 11 b_t2g (equation 9)
8.08262913966E+01 0 12 c_t2g (equation 9)
0.00000000000E+00 1 13 d_t2g (equation 9)
1.99140354046E-02 0 14 a_eg (equation 9)
3.46551434776E-01 0 15 b_eg (equation 9)
8.08262913966E+01 0 16 c_eg (equation 9)
0.00000000000E+00 1 17 d_eg (equation 9)
-9.10328414400E+00 0 18 e_{ss sigma} (equation 11) (Hamiltonian)
5.17873222758E-01 0 19 f_{ss sigma} (equation 11) (Hamiltonian)
0.00000000000E+00 1 20 fbar_{ss sigma} (equation 11) (Hamiltonian)
9.46662011248E-01 0 21 g_{ss sigma} (equation 11) (Hamiltonian)
3.10062713161E+00 0 22 e_{sp sigma} (equation 11) (Hamiltonian)
-1.14986950324E-01 0 23 f_{sp sigma} (equation 11) (Hamiltonian)
0.00000000000E+00 1 24 fbar_{sp sigma} (equation 11) (Hamiltonian)
8.16823694041E-01 0 25 g_{sp sigma} (equation 11) (Hamiltonian)
1.08944420501E+00 0 26 e_{pp sigma} (equation 11) (Hamiltonian)
8.81042934823E-02 0 27 f_{pp sigma} (equation 11) (Hamiltonian)
0.00000000000E+00 1 28 fbar_{pp sigma} (equation 11) (Hamiltonian)
7.44047706326E-01 0 29 g_{pp sigma} (equation 11) (Hamiltonian)
-3.47450944858E+00 0 30 e_{pp pi} (equation 11) (Hamiltonian)
4.87501025402E-01 0 31 f_{pp pi} (equation 11) (Hamiltonian)
0.00000000000E+00 1 32 fbar_{pp pi} (equation 11) (Hamiltonian)
8.54244679374E-01 0 33 g_{pp pi} (equation 11) (Hamiltonian)
-2.32021648963E+00 0 34 e_{sd sigma} (equation 11) (Hamiltonian)
-3.15365861097E-02 0 35 f_{sd sigma} (equation 11) (Hamiltonian)
0.00000000000E+00 1 36 fbar_{sd sigma} (equation 11) (Hamiltonian)
9.25016281342E-01 0 37 g_{sd sigma} (equation 11) (Hamiltonian)
-8.93441918651E-01 0 38 e_{pd sigma} (equation 11) (Hamiltonian)
6.29552973893E-02 0 39 f_{pd sigma} (equation 11) (Hamiltonian)
0.00000000000E+00 1 40 fbar_{pd sigma} (equation 11) (Hamiltonian)
7.37891092773E-01 0 41 g_{pd sigma} (equation 11) (Hamiltonian)
-5.40576594803E+00 0 42 e_{pd pi} (equation 11) (Hamiltonian)
2.97343282536E+00 0 43 f_{pd pi} (equation 11) (Hamiltonian)
0.00000000000E+00 1 44 fbar_{pd pi} (equation 11) (Hamiltonian)
1.11838057144E+00 0 45 g_{pd pi} (equation 11) (Hamiltonian)
-1.76353510091E+00 0 46 e_{dd sigma} (equation 11) (Hamiltonian)
1.19111234449E-01 0 47 f_{dd sigma} (equation 11) (Hamiltonian)
0.00000000000E+00 1 48 fbar_{dd sigma} (equation 11) (Hamiltonian)
8.86269873950E-01 0 49 g_{dd sigma} (equation 11) (Hamiltonian)
4.33011070171E+00 0 50 e_{dd pi} (equation 11) (Hamiltonian)
1.60095701629E-01 0 51 f_{dd pi} (equation 11) (Hamiltonian)
0.00000000000E+00 1 52 fbar_{dd pi} (equation 11) (Hamiltonian)
1.08523543274E+00 0 53 g_{dd pi} (equation 11) (Hamiltonian)
8.61842136416E+00 0 54 e_{dd delta} (equation 11) (Hamiltonian)
-3.97339261135E+00 0 55 f_{dd delta} (equation 11) (Hamiltonian)
0.00000000000E+00 1 56 fbar_{dd delta} (equation 11) (Hamiltonian)
1.29257807974E+00 0 57 g_{dd delta} (equation 11) (Hamiltonian)
-4.62972771140E+00 0 58 e_{ss sigma} (equation 11) (Overlap)
9.47334015518E+00 0 59 f_{ss sigma} (equation 11) (Overlap)
0.00000000000E+00 1 60 fbar_{ss sigma} (equation 11) (Overlap)
1.14594187503E+00 0 61 g_{ss sigma} (equation 11) (Overlap)
-7.76506172706E+00 0 62 e_{sp sigma} (equation 11) (Overlap)
-7.02630525419E-01 0 63 f_{sp sigma} (equation 11) (Overlap)
0.00000000000E+00 1 64 fbar_{sp sigma} (equation 11) (Overlap)
9.74542956783E-01 0 65 g_{sp sigma} (equation 11) (Overlap)
-8.67145638940E-01 0 66 e_{pp sigma} (equation 11) (Overlap)
2.08503648647E-03 0 67 f_{pp sigma} (equation 11) (Overlap)
0.00000000000E+00 1 68 fbar_{pp sigma} (equation 11) (Overlap)
6.06850104373E-01 0 69 g_{pp sigma} (equation 11) (Overlap)
4.59109295666E-02 0 70 e_{pp pi} (equation 11) (Overlap)
5.34381165673E-02 0 71 f_{pp pi} (equation 11) (Overlap)
0.00000000000E+00 1 72 fbar_{pp pi} (equation 11) (Overlap)
6.65480180637E-01 0 73 g_{pp pi} (equation 11) (Overlap)
6.33227165093E+00 0 74 e_{sd sigma} (equation 11) (Overlap)
1.08482522687E+00 0 75 f_{sd sigma} (equation 11) (Overlap)
0.00000000000E+00 1 76 fbar_{sd sigma} (equation 11) (Overlap)
1.12243836659E+00 0 77 g_{sd sigma} (equation 11) (Overlap)
-3.61229839778E+00 0 78 e_{pd sigma} (equation 11) (Overlap)
2.03039543811E-01 0 79 f_{pd sigma} (equation 11) (Overlap)
0.00000000000E+00 1 80 fbar_{pd sigma} (equation 11) (Overlap)
9.56355983487E-01 0 81 g_{pd sigma} (equation 11) (Overlap)
-3.42670301782E+02 0 82 e_{pd pi} (equation 11) (Overlap)
-5.22754450519E+01 0 83 f_{pd pi} (equation 11) (Overlap)
0.00000000000E+00 1 84 fbar_{pd pi} (equation 11) (Overlap)
1.51831050681E+00 0 85 g_{pd pi} (equation 11) (Overlap)
-1.72505694381E+03 0 86 e_{dd sigma} (equation 11) (Overlap)
4.47319803867E+02 0 87 f_{dd sigma} (equation 11) (Overlap)
0.00000000000E+00 1 88 fbar_{dd sigma} (equation 11) (Overlap)
1.53712769046E+00 0 89 g_{dd sigma} (equation 11) (Overlap)
-6.49992657214E-01 0 90 e_{dd pi} (equation 11) (Overlap)
-3.47252277946E-01 0 91 f_{dd pi} (equation 11) (Overlap)
0.00000000000E+00 1 92 fbar_{dd pi} (equation 11) (Overlap)
1.08398267722E+00 0 93 g_{dd pi} (equation 11) (Overlap)
2.17111542861E+01 0 94 e_{dd delta} (equation 11) (Overlap)
-4.38355657085E+00 0 95 f_{dd delta} (equation 11) (Overlap)
0.00000000000E+00 1 96 fbar_{dd delta} (equation 11) (Overlap)
1.18724223365E+00 0 97 g_{dd delta} (equation 11) (Overlap)
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