first try at implementing bond-order calculations #672

zerothi · 2024-01-21T08:26:37Z

This fixes #507 by adding the Wiberg and Mayer implementations.

I am not fully sure the Mayer is correct, since the expressions are PS_abPS_ba, but due to symmetry, I would expect this to be PS_ab ** 2.

@tfrederiksen would you please have a look at whether this makes sense? I am a bit puzzled about the Mayer implementation, it just looks the same as Wiberg, except the overlap matrix, and perhaps Mayer should be the default.

Closes Bond orders from DensityMatrix #507
Added tests for new/changed functions?
Ran isort . and black . at top-level
Documentation for functionality in docs/
Changes documented in CHANGELOG.md

src/sisl/physics/densitymatrix.py

codecov · 2024-01-21T14:20:32Z

Codecov Report

Attention: Patch coverage is 84.73282% with 20 lines in your changes are missing coverage. Please review.

Project coverage is 75.71%. Comparing base (2836e38) to head (b65bbe8).
Report is 3 commits behind head on main.

Files	Patch %	Lines
src/sisl/physics/densitymatrix.py	81.73%	19 Missing ⚠️
src/sisl/_core/sparse.py	92.30%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #672      +/-   ##
==========================================
+ Coverage   75.68%   75.71%   +0.02%     
==========================================
  Files         398      398              
  Lines       50418    50547     +129     
==========================================
+ Hits        38161    38270     +109     
- Misses      12257    12277      +20

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

src/sisl/io/siesta/_help.py

src/sisl/sparse.py

src/sisl/physics/densitymatrix.py

tfrederiksen · 2024-02-02T12:23:05Z

Thanks @zerothi, apologies for this late response. I just took a look now and tested the methods for a benzene molecule. This is what I got:

import sisl

dm = sisl.get_sile('benzene/RUN.fdf').read_density_matrix()

def calcBO(method):
    print(f"method={method}:")
    bo = dm.bond_order(method=method)
    for i in range(bo.na):
        print(bo.atoms[i].symbol, end=" ")
        #for j in range(bo.na):
        for j in range(i + 1):
            print(f"{bo[i, j]:5.2f}", end=" ")
        print()

calcBO("mayer")
calcBO("wiberg")
calcBO("bond+anti")

that produces

method=mayer:
C  0.42 
C  0.01  0.39 
C  0.01  0.00  0.40 
C  0.00  0.01  0.00  0.40 
C  0.00  0.00  0.01  0.00  0.39 
C  0.00  0.00  0.00  0.01  0.01  0.42 
H  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.00  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
method=wiberg:
C 25.27 
C  6.24 25.27 
C  6.25  0.71 25.27 
C  0.70  6.24  0.26 25.27 
C  0.71  0.26  6.24  0.71 25.27 
C  0.26  0.71  0.70  6.25  6.24 25.27 
H  5.26  0.65  0.65  0.01  0.01  0.00  8.78 
H  0.65  5.27  0.01  0.65  0.00  0.01  0.18  8.78 
H  0.65  0.01  5.27  0.00  0.65  0.01  0.18  0.00  8.78 
H  0.01  0.65  0.00  5.27  0.01  0.65  0.00  0.18  0.00  8.78 
H  0.01  0.00  0.65  0.01  5.27  0.65  0.00  0.00  0.18  0.00  8.78 
H  0.00  0.01  0.01  0.65  0.65  5.26  0.00  0.00  0.00  0.18  0.18  8.78 
method=bond+anti:
C  1.13 
C  0.27  1.13 
C  0.27  0.01  1.13 
C  0.01  0.27 -0.00  1.13 
C  0.01 -0.00  0.27  0.01  1.13 
C -0.00  0.01  0.01  0.27  0.27  1.13 
H  0.20 -0.00 -0.00  0.00  0.00  0.00  0.42 
H -0.00  0.20  0.00 -0.00  0.00  0.00 -0.00  0.42 
H -0.00  0.00  0.20  0.00 -0.00  0.00 -0.00 -0.00  0.42 
H  0.00 -0.00  0.00  0.20  0.00 -0.00 -0.00 -0.00  0.00  0.42 
H  0.00  0.00 -0.00  0.00  0.20 -0.00 -0.00  0.00 -0.00 -0.00  0.42 
H  0.00  0.00  0.00 -0.00 -0.00  0.20  0.00 -0.00 -0.00 -0.00 -0.00  0.42

I don't quite understand this as for benzene I would expect to find (quoting from Wikipedia/Bond_order):

In benzene, the delocalized molecular orbitals contain 6 pi electrons over six carbons, essentially yielding half a pi bond together with the sigma bond for each pair of carbon atoms, giving a calculated bond order of 1.5 (one and a half bond).

None of the three methods provide approx. the value 1.5 for the C-C bonds. Do you understand what is going on?

tfrederiksen · 2024-02-02T12:33:02Z

PS If I read the DM from a spin-polarized calculation I get completely different results for wiberg (although benzene is closed shell). mayer and bond+anti appear to be identical to the unpolarized calculation reported above.

method=mayer:
C  0.42 
C  0.01  0.39 
C  0.01  0.00  0.40 
C  0.00  0.01  0.00  0.40 
C  0.00  0.00  0.01  0.00  0.39 
C  0.00  0.00  0.00  0.01  0.01  0.42 
H  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
H  0.00  0.00  0.00  0.00  0.00  0.02  0.00  0.00  0.00  0.00  0.00  0.26 
method=wiberg:
C  0.14 
C  0.05  0.15 
C  0.05  0.00  0.15 
C  0.00  0.05  0.01  0.15 
C  0.00  0.01  0.05  0.00  0.15 
C  0.01  0.00  0.00  0.05  0.05  0.14 
H  0.06  0.00  0.00  0.00  0.00  0.00  0.07 
H  0.00  0.06  0.00  0.00  0.00  0.00  0.00  0.07 
H  0.00  0.00  0.06  0.00  0.00  0.00  0.00  0.00  0.07 
H  0.00  0.00  0.00  0.06  0.00  0.00  0.00  0.00  0.00  0.07 
H  0.00  0.00  0.00  0.00  0.06  0.00  0.00  0.00  0.00  0.00  0.07 
H  0.00  0.00  0.00  0.00  0.00  0.06  0.00  0.00  0.00  0.00  0.00  0.07 
method=bond+anti:
C  1.13 
C  0.27  1.13 
C  0.27  0.01  1.13 
C  0.01  0.27 -0.00  1.13 
C  0.01 -0.00  0.27  0.01  1.13 
C -0.00  0.01  0.01  0.27  0.27  1.13 
H  0.20 -0.00 -0.00  0.00  0.00  0.00  0.42 
H -0.00  0.20  0.00 -0.00  0.00  0.00 -0.00  0.42 
H -0.00  0.00  0.20  0.00 -0.00  0.00 -0.00 -0.00  0.42 
H  0.00 -0.00  0.00  0.20  0.00 -0.00 -0.00 -0.00  0.00  0.42 
H  0.00  0.00 -0.00  0.00  0.20 -0.00 -0.00  0.00 -0.00 -0.00  0.42 
H  0.00  0.00  0.00 -0.00 -0.00  0.20  0.00 -0.00 -0.00 -0.00 -0.00  0.42

tfrederiksen · 2024-02-02T14:13:48Z

As a reference, running ORCA for benzene produces these Mayer charges and bond orders in the output file:

  NA   - Mulliken gross atomic population
  ZA   - Total nuclear charge
  QA   - Mulliken gross atomic charge
  VA   - Mayer's total valence
  BVA  - Mayer's bonded valence
  FA   - Mayer's free valence

  ATOM       NA         ZA         QA         VA         BVA        FA
  0 C      6.1010     6.0000    -0.1010     3.9514     3.9514    -0.0000
  1 C      6.1012     6.0000    -0.1012     3.9515     3.9515    -0.0000
  2 C      6.1014     6.0000    -0.1014     3.9515     3.9515    -0.0000
  3 C      6.1014     6.0000    -0.1014     3.9515     3.9515    -0.0000
  4 C      6.1012     6.0000    -0.1012     3.9515     3.9515     0.0000
  5 C      6.1010     6.0000    -0.1010     3.9514     3.9514    -0.0000
  6 H      0.8988     1.0000     0.1012     0.9652     0.9652    -0.0000
  7 H      0.8988     1.0000     0.1012     0.9652     0.9652     0.0000
  8 H      0.8988     1.0000     0.1012     0.9652     0.9652    -0.0000
  9 H      0.8988     1.0000     0.1012     0.9652     0.9652     0.0000
 10 H      0.8988     1.0000     0.1012     0.9652     0.9652     0.0000
 11 H      0.8988     1.0000     0.1012     0.9652     0.9652    -0.0000

  Mayer bond orders larger than 0.100000
B(  0-C ,  1-C ) :   1.4171 B(  0-C ,  2-C ) :   1.4171 B(  0-C ,  6-H ) :   0.9584
B(  1-C ,  3-C ) :   1.4172 B(  1-C ,  7-H ) :   0.9584 B(  2-C ,  4-C ) :   1.4172
B(  2-C ,  8-H ) :   0.9583 B(  3-C ,  5-C ) :   1.4171 B(  3-C ,  9-H ) :   0.9584
B(  4-C ,  5-C ) :   1.4171 B(  4-C , 10-H ) :   0.9584 B(  5-C , 11-H ) :   0.9584

I think these numbers make: ~1.5 for C-C resonant bonds and ~1 for C-H single bonds.

zerothi · 2024-02-13T14:28:07Z

Thanks @tfrederiksen I have found the problem (it had to do with how the formula should be understood, MM vs simple multiplications).

I just have to generalize it for supercells so it works for chains etc.

src/sisl/physics/densitymatrix.py


 from .sparse import SparseOrbitalBZSpin
 from .spin import Spin

 __all__ = ["DensityMatrix"]


+def _get_density(DM, orthogonal, what="sum"):


zerothi · 2024-02-27T13:01:23Z

@tfrederiksen could you have a look again. I believe it is better now, I get this with Benzene and a Cchain:

Benzene:
C  1.39  0.09  0.10  0.09  1.39  0.99  0.07  0.01  0.01  0.01  0.07 
C  1.39  0.09  0.10  0.09  0.07  0.99  0.07  0.01  0.01  0.01 
C  1.39  0.09  0.10  0.01  0.07  0.99  0.07  0.01  0.01 
C  1.39  0.09  0.01  0.01  0.07  0.99  0.07  0.01 
C  1.39  0.01  0.01  0.01  0.07  0.99  0.07 
C  0.07  0.01  0.01  0.01  0.07  0.99 
H  0.01  0.00  0.00  0.00  0.01 
H  0.01  0.00  0.00  0.00 
H  0.01  0.00  0.00 
H  0.01  0.00 
H  0.01 
H 


Cchain:
method=mayer:
C  0.01  0.07  0.13  1.84  1.84  0.13  0.07  0.01

src/sisl/_core/sparse.py

@@ -57,24 +57,44 @@
 __all__ = ["SparseCSR", "ispmatrix", "ispmatrixd"]


-def _rows_and_cols(csr, rows=None):
-    """Retrieve the sparse patterns rows and columns from the sparse matrix
+def _to_coo(csr, data: bool = True, rows=None):


src/sisl/io/siesta/_help.py

src/sisl/physics/densitymatrix.py

+                        # the matrix is 0. Hence we just neglect that contribution.
+                        j = latt.sc_index(sc)
+                        r = r + Al[i] @ Bl[j]
+                    except:


This fixes #507 by adding the Wiberg and Mayer implementations. I am not fully sure the Mayer is correct, since the expressions are PS_abPS_ba, but due to symmetry, I would expect this to be PS_ab ** 2. fixed bond+antibond method, factor 0.5 Signed-off-by: Nick Papior <[email protected]>

Still needs a bit refinement, but it should be there now. Signed-off-by: Nick Papior <[email protected]>

Also corrected Wiberg (which gives bad results) Signed-off-by: Nick Papior <[email protected]>

While the mulliken bond-order can easily be calculated from the mulliken output, this will make it simpler. Signed-off-by: Nick Papior <[email protected]>

While it is a bit weird to have bond_order return orbital-order, I think it is not necessary to create a new method to retrieve the bond-order. Better to keep it simple. Signed-off-by: Nick Papior <[email protected]>

zerothi · 2024-03-01T21:09:07Z

I'll merge this, I think it looks correct, @tfrederiksen if/when you get the time, a check from your side would be grateful. For now I think it is OK to put in and let people play with it :)

Thanks!

tfrederiksen · 2024-03-08T10:10:23Z

I finally got to test this and it looks good to me too.

For benzene, I now get this:

benzene/RUN.fdf method=mayer
C  3.38 
C  1.38  3.38 
C  1.38  0.08  3.38 
C  0.08  1.38  0.10  3.38 
C  0.08  0.10  1.38  0.08  3.38 
C  0.10  0.08  0.08  1.38  1.38  3.38 
H  1.01  0.05  0.05  0.01  0.01  0.01  1.30 
H  0.05  1.01  0.01  0.05  0.01  0.01  0.01  1.30 
H  0.05  0.01  1.01  0.01  0.05  0.01  0.01  0.00  1.30 
H  0.01  0.05  0.01  1.01  0.01  0.05  0.00  0.01  0.00  1.30 
H  0.01  0.01  0.05  0.01  1.01  0.05  0.00  0.00  0.01  0.00  1.30 
H  0.01  0.01  0.01  0.05  0.05  1.01  0.00  0.00  0.00  0.01  0.01  1.30 
benzene/RUN.fdf method=wiberg
C  0.58 
C  0.19  0.58 
C  0.19  0.02  0.58 
C  0.02  0.19  0.04  0.58 
C  0.02  0.04  0.19  0.02  0.58 
C  0.04  0.02  0.02  0.19  0.19  0.58 
H  0.22  0.01  0.01  0.00  0.00  0.00  0.27 
H  0.01  0.23  0.00  0.01  0.00  0.00  0.00  0.27 
H  0.01  0.00  0.22  0.00  0.01  0.00  0.00  0.00  0.27 
H  0.00  0.01  0.00  0.22  0.00  0.01  0.00  0.00  0.00  0.27 
H  0.00  0.00  0.01  0.00  0.23  0.01  0.00  0.00  0.00  0.00  0.27 
H  0.00  0.00  0.00  0.01  0.01  0.22  0.00  0.00  0.00  0.00  0.00  0.27 
benzene/RUN.fdf method=mulliken
C  4.52 
C  1.08  4.52 
C  1.08  0.04  4.52 
C  0.04  1.08 -0.00  4.52 
C  0.04 -0.00  1.08  0.04  4.52 
C -0.00  0.04  0.04  1.08  1.08  4.52 
H  0.80 -0.01 -0.01  0.00  0.00  0.00  1.68 
H -0.01  0.80  0.00 -0.01  0.00  0.00 -0.00  1.68 
H -0.01  0.00  0.80  0.00 -0.01  0.00 -0.00 -0.00  1.68 
H  0.00 -0.01  0.00  0.80  0.00 -0.01 -0.00 -0.00  0.00  1.68 
H  0.00  0.00 -0.01  0.00  0.80 -0.01 -0.00  0.00 -0.00 -0.00  1.68 
H  0.00  0.00  0.00 -0.01 -0.01  0.80  0.00 -0.00 -0.00 -0.00 -0.00  1.68

With the :spin option I just get zeros, which I suppose is the correct result for this closed-shell molecule.

For [2]-triangulene, which has a S=1/2 ground state, I find among the carbons:

2T/RUN.fdf method=mayer
C  3.38 
C  1.38  3.41 
C  1.38  0.07  3.41 
C  0.07  1.27  0.06  3.58 
C  0.07  0.06  1.27  0.06  3.58 
C  0.02  0.07  0.00  1.27  0.01  3.41 
C  0.06  0.06  0.06  1.26  1.26  0.06  3.63 
C  0.02  0.00  0.07  0.01  1.27  0.00  0.06  3.41 
C  0.00  0.02  0.01  0.07  0.00  1.38  0.06  0.01  3.38 
C  0.00  0.01  0.01  0.06  0.06  0.06  1.26  0.06  0.07  3.58 
C  0.00  0.01  0.02  0.00  0.07  0.01  0.06  1.38  0.00  0.07  3.38 
C  0.01  0.00  0.00  0.06  0.01  0.07  0.06  0.00  1.38  1.27  0.02  3.41 
C  0.01  0.00  0.00  0.01  0.06  0.00  0.06  0.07  0.02  1.27  1.38  0.07  3.41 
2T/RUN.fdf method=wiberg
C  0.58 
C  0.19  0.62 
C  0.19  0.02  0.62 
C  0.02  0.16  0.03  0.45 
C  0.02  0.03  0.16  0.01  0.45 
C  0.01  0.02  0.00  0.16  0.01  0.62 
C  0.03  0.01  0.01  0.15  0.15  0.01  0.48 
C  0.01  0.00  0.02  0.01  0.16  0.00  0.01  0.62 
C  0.00  0.01  0.01  0.02  0.00  0.19  0.03  0.01  0.58 
C  0.00  0.01  0.01  0.01  0.01  0.03  0.15  0.03  0.02  0.45 
C  0.00  0.01  0.01  0.00  0.02  0.01  0.03  0.19  0.00  0.02  0.58 
C  0.01  0.00  0.00  0.03  0.01  0.02  0.01  0.00  0.19  0.16  0.01  0.62 
C  0.01  0.00  0.00  0.01  0.03  0.00  0.01  0.02  0.01  0.16  0.19  0.02  0.62 
2T/RUN.fdf method=mulliken
C  4.52 
C  1.09  4.60 
C  1.09  0.03  4.60 
C  0.03  1.03  0.00  4.74 
C  0.03  0.00  1.03  0.02  4.74 
C  0.00  0.02 -0.00  1.03  0.00  4.60 
C  0.00  0.02  0.02  1.01  1.01  0.02  4.81 
C  0.00 -0.00  0.02  0.00  1.03  0.00  0.02  4.60 
C  0.00  0.00  0.00  0.03 -0.00  1.09  0.00  0.00  4.52 
C -0.00  0.00  0.00  0.02  0.02  0.00  1.01  0.00  0.03  4.74 
C  0.00  0.00  0.00 -0.00  0.03  0.00  0.00  1.09  0.00  0.03  4.52 
C  0.00 -0.00  0.00  0.00  0.00  0.03  0.02 -0.00  1.09  1.03  0.00  4.60 
C  0.00  0.00 -0.00  0.00  0.00 -0.00  0.02  0.03  0.00  1.03  1.09  0.02  4.60

and some nonzero "spin-z" components:

2T/RUN.fdf method=mayer:spin
C  0.00 
C  0.00  0.03 
C  0.00  0.02  0.03 
C  0.00  0.00  0.00  0.00 
C  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.02  0.02  0.00  0.00  0.03 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.02  0.02  0.00  0.00  0.02  0.00  0.03 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.02  0.02  0.00  0.00  0.02  0.00  0.02  0.00  0.00  0.00  0.03 
C  0.00  0.02  0.02  0.00  0.00  0.02  0.00  0.02  0.00  0.00  0.00  0.02  0.03 
2T/RUN.fdf method=wiberg:spin
C  0.00 
C  0.00  0.01 
C  0.00  0.01  0.01 
C  0.00  0.00  0.00  0.00 
C  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.01  0.01  0.00  0.00  0.01 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.01  0.01  0.00  0.00  0.01  0.00  0.01 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
C  0.00  0.01  0.01  0.00  0.00  0.01  0.00  0.01  0.00  0.00  0.00  0.01 
C  0.00  0.01  0.01  0.00  0.00  0.01  0.00  0.01  0.00  0.00  0.00  0.01  0.01 
2T/RUN.fdf method=mulliken:spin
C -0.08 
C  0.01  0.38 
C  0.01 -0.01  0.38 
C  0.00  0.01 -0.00 -0.07 
C  0.00 -0.00  0.01  0.00 -0.07 
C -0.00 -0.01  0.00  0.01  0.00  0.38 
C -0.00 -0.00 -0.00 -0.00 -0.00 -0.00  0.02 
C -0.00  0.00 -0.01  0.00  0.01 -0.00 -0.00  0.38 
C  0.00 -0.00  0.00  0.00  0.00  0.01 -0.00  0.00 -0.08 
C  0.00  0.00  0.00  0.00  0.00 -0.00 -0.00 -0.00  0.00 -0.07 
C  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.01  0.00  0.00 -0.08 
C  0.00  0.00 -0.00 -0.00  0.00 -0.01 -0.00  0.00  0.01  0.01 -0.00  0.38 
C  0.00 -0.00  0.00  0.00 -0.00  0.00 -0.00 -0.01 -0.00  0.01  0.01 -0.01  0.38

Not sure what to take away from the latter, though.

zerothi · 2024-03-08T10:21:16Z

Thanks for following up. Yeah, I am not sure about the spin details. But I guess they can be used to correlate differences between two structures/states.

I would assume it means something is the spin configuration is a localized or delocalized quantity.

github-advanced-security bot found potential problems Jan 21, 2024

View reviewed changes

src/sisl/physics/densitymatrix.py Fixed Show fixed Hide fixed

zerothi force-pushed the 507-bond-order branch from 28bf115 to 9bad0c3 Compare January 21, 2024 14:12

zerothi mentioned this pull request Jan 21, 2024

Bond orders from DensityMatrix #507

Closed

github-advanced-security bot found potential problems Jan 21, 2024

View reviewed changes

src/sisl/io/siesta/_help.py Fixed Show fixed Hide fixed

src/sisl/sparse.py Fixed Show fixed Hide fixed

src/sisl/physics/densitymatrix.py Fixed Show fixed Hide fixed

zerothi force-pushed the 507-bond-order branch from f5a6fa9 to 2a38fd7 Compare February 27, 2024 12:44

github-advanced-security bot found potential problems Feb 27, 2024

View reviewed changes

github-advanced-security bot found potential problems Feb 28, 2024

View reviewed changes

src/sisl/physics/densitymatrix.py

# the matrix is 0. Hence we just neglect that contribution.

j = latt.sc_index(sc)

r = r + Al[i] @ Bl[j]

except:

Check notice

Code scanning / CodeQL

Except block handles 'BaseException' Note

Except block directly handles BaseException.

zerothi force-pushed the 507-bond-order branch from f794455 to aa84152 Compare February 28, 2024 11:18

zerothi added 4 commits February 28, 2024 21:42

fixed bond-order calculations for wiberg and mayer

54e2cf6

Still needs a bit refinement, but it should be there now. Signed-off-by: Nick Papior <[email protected]>

speeded up large system calculations

ee5fd31

Also corrected Wiberg (which gives bad results) Signed-off-by: Nick Papior <[email protected]>

added Mulliken bond-order

40907da

While the mulliken bond-order can easily be calculated from the mulliken output, this will make it simpler. Signed-off-by: Nick Papior <[email protected]>

zerothi force-pushed the 507-bond-order branch from 589bee7 to 40907da Compare February 28, 2024 20:42

added orbital projection to bond-order

b65bbe8

While it is a bit weird to have bond_order return orbital-order, I think it is not necessary to create a new method to retrieve the bond-order. Better to keep it simple. Signed-off-by: Nick Papior <[email protected]>

zerothi merged commit 6844de2 into main Mar 1, 2024
8 checks passed

zerothi deleted the 507-bond-order branch March 1, 2024 21:09

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

first try at implementing bond-order calculations #672

first try at implementing bond-order calculations #672

zerothi commented Jan 21, 2024

codecov bot commented Jan 21, 2024 •

edited

Loading

tfrederiksen commented Feb 2, 2024

tfrederiksen commented Feb 2, 2024 •

edited

Loading

tfrederiksen commented Feb 2, 2024 •

edited

Loading

zerothi commented Feb 13, 2024

zerothi commented Feb 27, 2024 •

edited

Loading

zerothi commented Mar 1, 2024

tfrederiksen commented Mar 8, 2024

zerothi commented Mar 8, 2024

first try at implementing bond-order calculations #672

first try at implementing bond-order calculations #672

Conversation

zerothi commented Jan 21, 2024

codecov bot commented Jan 21, 2024 • edited Loading

Codecov Report

tfrederiksen commented Feb 2, 2024

tfrederiksen commented Feb 2, 2024 • edited Loading

tfrederiksen commented Feb 2, 2024 • edited Loading

zerothi commented Feb 13, 2024

zerothi commented Feb 27, 2024 • edited Loading

zerothi commented Mar 1, 2024

tfrederiksen commented Mar 8, 2024

zerothi commented Mar 8, 2024

codecov bot commented Jan 21, 2024 •

edited

Loading

tfrederiksen commented Feb 2, 2024 •

edited

Loading

tfrederiksen commented Feb 2, 2024 •

edited

Loading

zerothi commented Feb 27, 2024 •

edited

Loading