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

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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.

add: test for unrestricted Turbomole calculation

to hopefully make them avaiable for nix

as scipy shifted the whole fragment's centroid into the origin, which was bad. Actually, the fragment must be shifted in a way, so the anchor atom is in the origin.

mod: set overachieve factor 3 in hindered_rotor opts

now convergence of partition function and predicted standard deviation are checked.

instead of np.int64

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

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

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

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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

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

fix: scan_factors were wrong for RDClass2

f848c14

fix: plotting Marcus scan and model

685e0e4

fix: added missing import in io.hessian

aac8a4a

add: epos from plain Mulliken, violin plots from Wigner sampling

696fb54

fix: calculation of normal coordinates was wrong

564a8bc

mod: also keep unrestricted CI-vectors

7dffc84

add: test for unrestricted Turbomole calculation

Johannes Steinmetzer added 17 commits October 29, 2024 08:52

fix: add left/right_images to growing string test

96a4d72

fix: added more files to .gitgnore

30fcb70

to hopefully make them avaiable for nix

fix: rotation code was wrong

f879395

as scipy shifted the whole fragment's centroid into the origin, which was bad. Actually, the fragment must be shifted in a way, so the anchor atom is in the origin.

re-enabled alignment in hindered_rotor

0ef2cce

add reporting of single-point calc. timings in hindered_rotor

be5576f

add report after hindered_rotor calculation

c09fb35

add: manually halt hindered_rotor calc by touching 'converged_hr'

dd9b51b

mod: set overachieve factor 3 in hindered_rotor opts

mod: updated convergence check in hindered_rotor

884ecd6

now convergence of partition function and predicted standard deviation are checked.

fix: typed_prims contain normal use normal int indices again

c3e4948

instead of np.int64

mod/fix: always work on a copy of opt_kwargs in run_opt

c4e4dfe

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 12 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

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DMA, Local force constants, Marcus dimension #265

DMA, Local force constants, Marcus dimension #265

eljost commented Aug 7, 2023 •

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