DMA, Local force constants, Marcus dimension #265

eljost · 2023-08-07T14:41:16Z

removed deprecated and tests_staging
several bugfixes

scripts/gen_m2m.py

pysisyphus/wavefunction/dma.py

tests/test_dask/test_dask.py

+            "max_cycles": 1,
+        },
+    )
+    opt = opt_result.opt


codecov · 2023-08-08T13:07:20Z

Codecov Report

Attention: Patch coverage is 34.37692% with 4276 lines in your changes missing coverage. Please review.

Project coverage is 27.80%. Comparing base (5950976) to head (eda0102).
Report is 75 commits behind head on master.

❗ Current head eda0102 differs from pull request most recent head 8bd72d3

Please upload reports for the commit 8bd72d3 to get more accurate results.

❗ There is a different number of reports uploaded between BASE (5950976) and HEAD (eda0102). Click for more details.

HEAD has 53 uploads less than BASE
| Flag | BASE (5950976) | HEAD (eda0102) | |------|------|------| |unittests|54|1|

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #265       +/-   ##
===========================================
- Coverage   61.58%   27.80%   -33.78%     
===========================================
  Files         282      319       +37     
  Lines       29472    73521    +44049     
===========================================
+ Hits        18149    20440     +2291     
- Misses      11323    53081    +41758

Flag	Coverage Δ
unittests	`27.80% <34.37%> (-33.78%)`	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
pysisyphus/TablePrinter.py	`100.00% <100.00%> (ø)`
pysisyphus/__init__.py	`100.00% <100.00%> (ø)`
pysisyphus/calculators/AFIR.py	`89.82% <100.00%> (ø)`
pysisyphus/calculators/AnaPotBase.py	`55.14% <100.00%> (-0.21%)`	⬇️
pysisyphus/calculators/MOPAC.py	`28.71% <ø> (ø)`
pysisyphus/calculators/__init__.py	`100.00% <100.00%> (ø)`
pysisyphus/cos/NEB.py	`68.13% <ø> (ø)`
pysisyphus/drivers/afir.py	`33.04% <100.00%> (-0.22%)`	⬇️
pysisyphus/drivers/pka.py	`100.00% <100.00%> (ø)`
pysisyphus/helpers.py	`72.44% <100.00%> (-3.25%)`	⬇️
... and 102 more

... and 4 files with indirect coverage changes

pysisyphus/plot_ascii.py

+import warnings
+
+try:
+    import ase


github-advanced-security

CodeQL found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.

github-advanced-security

CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

currently tests Turbomole, ORCA and PySCF. Gaussian will follow shortly

now all OverlapCalculators return the GS energy when root is None

and added test

as originally described in #214. fix: pysisplot -o was broken

using functools.singledispatch

add: ability to scan transition states in hindered_rotor with appropriate opt_cls key add: hessian information is stored w/ correct prefix fix: calculation of force constant using periodic finite differences used one point too much

this gathers the "energy" values from JSON files produced by run_calculations and plots them

fix flake10/flake8 typo

previously, some bonds were defined two times

now the user can manually select the atoms belonging to a rotor by providing a "rotor:" subsection in the "hindered_rotor:" section mod: moved TorsionGPRResult dataclass to own module mod: hindered_rotor torsion_scan.trj is now aligned

would crash if thermoanalysis is not available

moved modules from pysisyphus.wavefunction and pysisyphus.drivers to the central subpackages pysisyphus.diabatization

mod: switch from print to logging

add: dumping of diabatic transition densities to diabatization HDF5 file

add: HALF diabatization for testing fix: adiabatic spin density cube fns are also returned

…l_data

eljost changed the title ~~Dev~~ DMA, Local force constants, Marcus dimension Aug 7, 2023

github-advanced-security bot found potential problems Aug 7, 2023

View reviewed changes

scripts/gen_m2m.py Fixed Show fixed Hide fixed

scripts/gen_m2m.py Fixed Show fixed Hide fixed

pysisyphus/wavefunction/dma.py Fixed Show fixed Hide fixed

github-advanced-security bot found potential problems Aug 8, 2023

View reviewed changes

tests/test_dask/test_dask.py

"max_cycles": 1,

},

)

opt = opt_result.opt

Check notice

Code scanning / CodeQL

Unused local variable Note test

Variable opt is not used.

eljost force-pushed the dev branch 2 times, most recently from 01215f3 to 494de1c Compare August 9, 2023 08:06

github-advanced-security bot found potential problems Aug 9, 2023

View reviewed changes

pysisyphus/plot_ascii.py

import warnings

try:

import ase

Check notice

Code scanning / CodeQL

Unused import Note

Import of 'ase' is not used.

github-advanced-security bot found potential problems Aug 18, 2023

View reviewed changes

eljost force-pushed the dev branch 3 times, most recently from 9c63d47 to 20d0884 Compare August 21, 2023 14:15

eljost force-pushed the dev branch 3 times, most recently from ec5fdb7 to 39f3968 Compare September 5, 2023 12:32

eljost force-pushed the dev branch from 5c25557 to d08c906 Compare September 26, 2023 14:36

eljost force-pushed the dev branch from e84c142 to 2a4a37f Compare October 9, 2023 13:02

eljost force-pushed the dev branch from 9bbd63d to d4c5c76 Compare November 10, 2023 12:49

github-advanced-security bot found potential problems Dec 18, 2023

View reviewed changes

eljost force-pushed the dev branch from 7261cf6 to ea800c6 Compare December 19, 2023 13:47

eljost force-pushed the dev branch 2 times, most recently from d950481 to 50a7f5c Compare January 17, 2024 08:40

eljost force-pushed the dev branch from 0b393a2 to 051238e Compare March 11, 2024 11:05

eljost force-pushed the dev branch from 96efe81 to f12295e Compare April 10, 2024 06:24

eljost force-pushed the dev branch from 9fe6572 to bea3f7f Compare September 5, 2024 11:30

Johannes Steinmetzer and others added 6 commits October 2, 2024 15:01

mod: implemented get_all_energies for PySCF and added a test

7d8c811

currently tests Turbomole, ORCA and PySCF. Gaussian will follow shortly

mod: implemented get_all_energies for Gaussian16 and added a test

b8b3af1

now all OverlapCalculators return the GS energy when root is None

add: get_all_energies() for DFTB+ calculator

f5fdd14

and added test

add: Solve min-cost-problem for better ES overlaps

c0097c0

as originally described in #214. fix: pysisplot -o was broken

mod: keep integration grid in dedicated dataclass

9caab3d

add: simple MolGrid construction from Wavefunction

3cbc0ef

using functools.singledispatch

Johannes Steinmetzer added 7 commits November 4, 2024 16:41

fix: fragmentation for hr with > 2 initial fragments

5390754

add: ability to scan transition states in hindered_rotor with appropriate opt_cls key add: hessian information is stored w/ correct prefix fix: calculation of force constant using periodic finite differences used one point too much

add: 'pysistrj --calcs' to plot results from plain calculations

382c396

this gathers the "energy" values from JSON files produced by run_calculations and plots them

fix: (hopefully) allow plotting of old IRC HDF5 files

968e882

fix: test fixes after xtb update to 6.7.1

79c89f6

mod: filter out eigenvectors w/ vanishing gradient

4947378

mod: exclude integrals from flake8

2b52800

mod: run pytest w/ --color=yes in github actions

ca7b83d

fix flake10/flake8 typo

eljost force-pushed the dev branch from bc3d501 to ca7b83d Compare November 5, 2024 14:08

Johannes Steinmetzer added 19 commits November 6, 2024 15:29

fix: further round of test fixes

78d214a

fix: don't add hydrogen_bonds that are already bonds

166dfcf

previously, some bonds were defined two times

mod: include trans-rot-projector in inverse of Wilson-B mat

bc03360

mod: keep constraints when rebuilding coordinates

d0aefaa

fix: enabling project_tr was a bad idea

41a03c3

fix: remove type hint from optional addon

5a70f9b

would crash if thermoanalysis is not available

fix: use capitalized atoms when converting to ASE

19e0491

add: "LINEAR" shortcut for creating linear bend & its complement

8352c1c

add: new diabatization driver

72eb2a9

mod: refactored diabatization

00f1d7e

moved modules from pysisyphus.wavefunction and pysisyphus.drivers to the central subpackages pysisyphus.diabatization

fix: make diabatization.driver importable w/o pysisyphus_addons

adc9c8f

mod: switch to HDF5 file for diabatization

e8bc3f1

mod: switch from print to logging

mod: dump more datasets to HDF5 file

0271f6d

mod: hdf5 data models now require a dtype

07085fc

add: dumping of diabatic transition densities to diabatization HDF5 file

mod: also write diabatization kinds to HDF5

201cab5

add: also consider spin-densities in chimerabatch

02b8a49

add: HALF diabatization for testing fix: adiabatic spin density cube fns are also returned

add: method to io.cube.Cube to createa new cube from ref. cube and vo…

38f7dd3

…l_data

fix: added missing h5_fn in dia driver test

a4b5b65

eljost force-pushed the dev branch from 00dea44 to a4b5b65 Compare November 25, 2024 12:42

Johannes Steinmetzer added 2 commits November 27, 2024 21:44

mod: report fragments in orca_ctnums.py

230b964

fix: mention files explicitly in .gitignore

2bae9fe

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

DMA, Local force constants, Marcus dimension #265

DMA, Local force constants, Marcus dimension #265

eljost commented Aug 7, 2023 •

edited

Loading

codecov bot commented Aug 8, 2023 •

edited

Loading

github-advanced-security bot left a comment

github-advanced-security bot left a comment

DMA, Local force constants, Marcus dimension #265

Are you sure you want to change the base?

DMA, Local force constants, Marcus dimension #265

Conversation

eljost commented Aug 7, 2023 • edited Loading

codecov bot commented Aug 8, 2023 • edited Loading

Codecov Report

github-advanced-security bot left a comment

Choose a reason for hiding this comment

github-advanced-security bot left a comment

Choose a reason for hiding this comment

eljost commented Aug 7, 2023 •

edited

Loading

codecov bot commented Aug 8, 2023 •

edited

Loading