Input Writer #188

FarnazH · 2020-08-20T05:59:40Z

This PR addresses issue #43.

Thewrite_input is added to api module.
The Gaussian input writer is added as an example and is tested with the default and user-defined input template.

evohringer

It seems all clear to me. Great!

iodata/api.py

iodata/inputs/gaussian.py

tovrstra

Thanks for the PR! I just have a few minor comments...

iodata/api.py

iodata/inputs/gaussian.py

tovrstra · 2020-08-23T15:27:38Z

iodata/inputs/orca.py

+
+
+def write_input(f: TextIO, data: IOData, template: str = None):
+    """Do not edit this docstring. It will be overwritten."""


Same comment as above regarding documentation decorator.

iodata/test/test_inputs.py

iodata/inputs/orca.py

lmacaya

Only minor comments, but I think the main functionality is complete. Work on the docstring is still pending, so I hope to collaborate on that this week.

lmacaya · 2020-09-01T19:48:58Z

iodata/inputs/gaussian.py

+    fields["charge"] = int(data.charge) if data.charge is not None else 0
+
+    # convert run type to Gaussian keywords
+    run_types = {"energy": "sp", "freq": "freq", "opt": "opt"}


Based in #202, we can update this dict to all the run_types supported in IOData.

lmacaya · 2020-09-01T19:49:58Z

iodata/inputs/orca.py

+    fields["run_type"] = data.run_type if data.run_type is not None else 'energy'
+    # convert spin polarization to multiplicity
+    fields["spinmult"] = int(data.spinpol) + 1 if data.spinpol is not None else 1
+    fields["charge"] = int(data.charge) if data.nelec is not None else 0


Suggested change

fields["charge"] = int(data.charge) if data.nelec is not None else 0

fields["charge"] = int(data.charge) if data.charge is not None else 0

lmacaya · 2020-09-02T02:14:07Z

iodata/inputs/orca.py

+    fields["obasis_name"] = data.obasis_name if data.obasis_name is not None else 'STO-3G'
+
+    # convert run type to orca keywords
+    run_types = {"energy": "Energy", "freq": "Freq", "opt": "Opt"}


Same as gaussian.py, we can update this dict.

tovrstra

Thanks for the updates. I've added a few small comments and I also have a few more general small requests:

Could you add the file header to iodata/inputs/__init__.py?
The initialization of the fields dictionary can be moved to a common.py module. This code can be reused by most formats.

(There are also some open comments from my previous review. If these are not clear, please let me know. I'll dig them up if needed.)

iodata/inputs/orca.py

codecov · 2020-09-02T22:55:18Z

Codecov Report

Merging #188 (0f628f8) into master (c8e8f10) will decrease coverage by 0.19%.
The diff coverage is 95.90%.

@@            Coverage Diff             @@
##           master     #188      +/-   ##
==========================================
- Coverage   95.76%   95.56%   -0.20%     
==========================================
  Files          63       65       +2     
  Lines        6752     6772      +20     
  Branches      865      860       -5     
==========================================
+ Hits         6466     6472       +6     
- Misses        129      139      +10     
- Partials      157      161       +4

Impacted Files	Coverage Δ
iodata/api.py	`86.11% <78.26%> (-4.09%)`	⬇️
iodata/docstrings.py	`96.66% <89.47%> (-3.34%)`	⬇️
iodata/inputs/common.py	`100.00% <100.00%> (ø)`
iodata/inputs/gaussian.py	`100.00% <100.00%> (ø)`
iodata/inputs/orca.py	`100.00% <100.00%> (ø)`
iodata/test/test_inputs.py	`100.00% <100.00%> (ø)`
iodata/formats/extxyz.py	`86.45% <0.00%> (-7.30%)`	⬇️
iodata/utils.py	`87.01% <0.00%> (-0.49%)`	⬇️
iodata/formats/molden.py	`91.30% <0.00%> (-0.03%)`	⬇️
iodata/test/test_molden.py	`99.24% <0.00%> (-0.01%)`	⬇️
... and 14 more

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tovrstra · 2020-09-03T06:39:28Z

(No need to worry about the code coverage failures. These reports are not always accurate but it does add useful comments in the code at times.)

PaulWAyers · 2021-03-11T04:30:27Z

@tovrstra @FarnazH can we get this moving? Several people in the group (@BradenDKelly @wilhadams @fwmeng88 Menna, @tczorro) all need this moving forward and are creating their own tools and duplicating work in its absence.

FanwangM · 2021-03-11T04:46:55Z

This is going to be a lovely feature! I like it as I hide my ugly scripts in a safe place.
Thank you!!

Edit: One short question: do we need to use basis_set_exchange to support a non-standard Gaussian basis set or the input module will take care of it? As far as what I have learned from the codes, my guess we have to put the basis set information in the template file.

tovrstra · 2021-03-11T07:03:27Z

I was looking into this a few days ago and wanted to go through it in short term, so yep. I'm picking this up shortly. Also other PRs need to be looked at. @fwmeng88 I'll come back to your question after having gone through the diff.

tovrstra · 2021-03-12T05:16:16Z

@fwmeng88 You are right any non-standard basis sets would have to be put in the template. This may seem easy at first, but there could be a potential difficulty. Gaussian may not run when given custom basis sets for elements not present in the geometry. If you want to run calculations on a database of molecules which vary in chemical composition, the template would need to be modified for each molecule specifically to just include basis functions for the chemical elements that are present. (This is what I remember from long time ago for an older version of Gaussian, so please double check with the latest version.)

tovrstra · 2021-03-12T10:14:50Z

It seems that the free plan of Travis is not exactly working for us. I've tested everything locally and things pass, so I'll merge. Eventually we may have to move away from Travis to get CI up and running again.

FanwangM · 2021-03-12T15:48:47Z

Just checked with the latest version of Gaussian g16/c.01 that we have to specify the basis set exactly only for the atoms that exist in a given molecule. So, things can be tough.

I have opened a new issue related to this with a more detailed explanation. #221
@tovrstra

PaulWAyers · 2021-03-12T17:29:34Z

It seems that the free plan of Travis is not exactly working for us. I've tested everything locally and things pass, so I'll merge. Eventually we may have to move away from Travis to get CI up and running again.

Perhaps we should go to GitHub Actions. Procrustes is using GitHub Actions. @fwmeng88 set that up for Procrustes.

FanwangM · 2021-03-12T19:30:21Z

It seems that the free plan of Travis is not exactly working for us. I've tested everything locally and things pass, so I'll merge. Eventually we may have to move away from Travis to get CI up and running again.

Perhaps we should go to GitHub Actions. Procrustes is using GitHub Actions. @fwmeng88 set that up for Procrustes.

It's not perfect yet but works nicely. https://github.com/theochem/procrustes/blob/master/.github/workflows/testing.yml

wilhadams and others added 4 commits August 19, 2020 15:36

Add Gaussian input writer

3c30091

Add write_input to api.py module

75e0b53

Test gaussian input writer using default template

41aa3eb

Test gaussian input writer using user template

0ea6726

FarnazH requested review from tovrstra, evohringer and wilhadams August 20, 2020 05:59

FarnazH added 2 commits August 20, 2020 00:04

Add __all__ to inputs/gaussian.py module

9e5b2e6

Fix pylint no-else-return and wrong-import-order

17d5c88

evohringer previously approved these changes Aug 20, 2020

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Fix docstring & update default values

2709a3e

FarnazH dismissed evohringer’s stale review via 2709a3e August 20, 2020 18:46

FarnazH mentioned this pull request Aug 21, 2020

Infrastructure for making input files for QC codes #43

Closed

FarnazH commented Aug 21, 2020

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lmacaya added 5 commits August 21, 2020 23:20

Add write_input function for orca

7cef0c9

Add tests for orca write_input

c4d733e

Add template for orca write_input testing

27a2a61

Add __init__.py for relative import

eb988c3

Add default docstring to gaussian write_input for future decorator

2a9961a

tovrstra mentioned this pull request Aug 23, 2020

Configurable atom lines in write_input #192

Open

tovrstra reviewed Aug 23, 2020

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tovrstra mentioned this pull request Aug 24, 2020

Convert all remaining namedtuples to attr classes #157

Closed

FarnazH added 6 commits August 24, 2020 11:51

Use attr.asdict in Gaussian input writer

e4eb9b2

Add expected test inputs to test/data/input_*.txt

713e410

Remove empty lines & unsed import in test_inputs

8319cf0

Add recurse=False in orca module & remove test fix

a87c0f2

Remove attrname argument of _select_input_module

23442ef

Fix pylint wrong-import-order

328f38b

lmacaya reviewed Aug 24, 2020

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tovrstra mentioned this pull request Aug 25, 2020

Fix "unsupported operand" issue when accessing IOData.charge #196

Merged

FarnazH requested review from evohringer, lmacaya and tovrstra September 1, 2020 18:12

lmacaya reviewed Sep 1, 2020

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lmacaya reviewed Sep 2, 2020

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tovrstra reviewed Sep 2, 2020

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Add header to __init__

0891a63

lmacaya added 5 commits September 3, 2020 21:42

Add write_input decorator and minor fixes

6027980

Update docstrings in api.py

22233a4

Add populate_fields func to common

6a97b0d

Reformat gaussian write_input

28c167c

Reformat orca write_input

0f628f8

tovrstra force-pushed the write_input branch from ee99dd0 to 0f628f8 Compare March 12, 2021 06:24

tovrstra and others added 2 commits March 12, 2021 07:27

Merge branch 'master' into write_input

2d32f4e

Fix minor issues and include input writer in docs

5c68134

tovrstra merged commit 8f1f591 into theochem:master Mar 12, 2021

FanwangM mentioned this pull request Mar 12, 2021

Support of non-standard basis set for Gaussian #221

Open

FarnazH deleted the write_input branch March 26, 2021 19:58

FarnazH restored the write_input branch March 26, 2021 19:58

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Input Writer #188

Input Writer #188

FarnazH commented Aug 20, 2020 •

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FanwangM commented Mar 11, 2021 •

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tovrstra commented Mar 11, 2021

tovrstra commented Mar 12, 2021

tovrstra commented Mar 12, 2021

FanwangM commented Mar 12, 2021

PaulWAyers commented Mar 12, 2021

FanwangM commented Mar 12, 2021



		def write_input(f: TextIO, data: IOData, template: str = None):
		"""Do not edit this docstring. It will be overwritten."""

	fields["charge"] = int(data.charge) if data.nelec is not None else 0
	fields["charge"] = int(data.charge) if data.charge is not None else 0

Input Writer #188

Input Writer #188

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