Fix `Atoms.cluster_from_file()` in `io.feff.inputs` giving wrong number of atoms #3426

kaifengZheng · 2023-10-26T16:42:55Z

Summary

Atoms.cluster_from_file() generates a cluster with a wrong number of atoms because it skips wrong lines when the format of feff input file in the Atom parts is different.
Major changes:

feature 1(old): skipped 3 lines from the line having "ATOMS"
fix 1(new): only skip 1 line(ignore ATOMS line)
feature 2(old): It requires the special format of FEFF input file
fix 2(new): add a condition to ignore the lines beginning with "*", which is feasible to adapt the different format of Atom parts

Checklist

Google format doc strings added. Check with ruff.
Type annotations included. Check with mypy.
Tests added for new features/fixes.
If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

This reverts commit 8112068.

update

…checks initialize PymatgenTest.TEST_STRUCTURES as dict[Path, None]

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

fix a bug

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

janosh · 2023-10-26T16:52:43Z

pymatgen/io/feff/inputs.py

        coords = []
        symbols = []
        for line in lines:
-            if line:
+            if line and line[0].__contains__("*"):


Suggested change

if line and line[0].__contains__("*"):

if line and line.startswith("*"):

janosh · 2023-10-26T16:53:11Z

tests/io/feff/test_inputs.py

+def test_atom_num(self):
+    atoms = Atoms.cluster_from_file("ATOMS_test.inp")
+    num_atom = 37
+    assert len(atoms) != num_atom


why not test for the expected number of atoms?

Hi Janosh,
The expected number of atoms is 37; how should I specify this value?

Is != a typo?

You're missing one level of indentation to make it a method of the test class.

Let me fix it. sorry to confuse you. I want it to pass when the expected number of atoms is equal to num_atom and throw an error when the numbers are not equal.

janosh · 2023-10-26T16:54:00Z

tests/files/ATOMS_test.inp

We have 6 or more existing .inp files. Can you reuse those for testing?

Every updated feff.inp file has the same format. My input file deletes the * lines under ATOMS, which can be used for the test.

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

janosh · 2023-10-27T16:30:24Z

tests/io/feff/test_inputs.py

+def test_atom_num(self):
+    atoms = Atoms.cluster_from_file("ATOMS_test.inp")
+    num_atom = 37
+    assert len(atoms) != num_atom


You're missing one level of indentation to make it a method of the test class.

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

janosh

This looks almost done but can you fix the failing tests: FileNotFoundError: [Errno 2] No such file or directory: 'ATOMS_test.inp'?

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

for line in lines: > if line and not line.startswith("*"):

kaifengZheng and others added 30 commits August 18, 2023 22:20

Update test_sets.py

1dc8c43

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

add test file

bb74a32

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

fix a bug in inputs.py

fac911d

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

pre-commit auto-fixes

0018837

files

8112068

Revert "files"

943cbd4

This reverts commit 8112068.

Merge branch 'materialsproject:master' into master

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Merge branch 'materialsproject:master' into master

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Merge branch 'materialsproject:master' into master

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Merge branch 'master' into master

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Merge branch 'materialsproject:master' into master

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Merge branch 'materialsproject:master' into master

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Merge branch 'materialsproject:master' into master

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Merge branch 'master' into master

ae62a3a

remove test file and modify the test method

3fd1904

pre-commit auto-fixes

84392b8

Merge branch 'master' of https://github.com/materialsproject/pymatgen

81c1ac5

update

Merge branch 'materialsproject:master' into master

ccb5106

Merge branch 'master' of https://github.com/kaifengZheng/pymatgen

19896dc

update

i->idx

91fab3c

Merge branch 'master' into master

ebcedfe

Merge branch 'master' into master

f036f0a

forgot to negate check_occu after inverting semantics from skip_occu_…

00da9c8

…checks initialize PymatgenTest.TEST_STRUCTURES as dict[Path, None]

Merge branch 'materialsproject:master' into master

cde0422

Update test_sets.py

bd25993

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

pre-commit auto-fixes

95c0b56

Merge branch 'master' into master

80b2ad4

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

pre-commit auto-fixes

c915adb

Update testing.py resolve conflict

844336e

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

Merge branch 'master' into master

61b5914

janosh and others added 8 commits August 22, 2023 09:50

add PR link to new test

6607fa7

Merge branch 'materialsproject:master' into master

e9c3d82

Merge branch 'materialsproject:master' into master

f8ef114

Merge branch 'materialsproject:master' into master

d2cfa6a

fix Atom.input miss atoms problem

cb05b84

Merge branch 'master' of https://github.com/kaifengZheng/pymatgen

6b14744

fix a bug

pre-commit auto-fixes

432a166

Update inputs.py

4a03535

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

janosh requested changes Oct 26, 2023

View reviewed changes

kaifengZheng added 3 commits October 26, 2023 15:07

Update inputs.py

9151dbd

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

Update inputs.py

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Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

Merge branch 'master' into master

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janosh requested changes Oct 27, 2023

View reviewed changes

kaifengZheng and others added 5 commits October 27, 2023 12:52

Merge branch 'materialsproject:master' into master

9f40a5b

Update test_inputs.py

bae05b1

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

pre-commit auto-fixes

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Merge branch 'master' into master

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Merge branch 'master' into master

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janosh requested changes Oct 31, 2023

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janosh added io Input/output functionality fix Bug fix PRs labels Oct 31, 2023

kaifengZheng and others added 5 commits October 31, 2023 12:27

Merge branch 'master' into master

dcf190c

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

Update test_inputs.py

614cc85

Signed-off-by: KaifengZheng <48105165+kaifengZheng@users.noreply.github.com>

fix AttributeError: 'list' object has no attribute 'startswith'

1d5214b

for line in lines: > if line and not line.startswith("*"):

gzip tests/files/ATOMS_test.inp

c346c00

improve test

dc1b939

janosh changed the title ~~Fix a bug in io.feff.inputs.Atoms~~ Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms Nov 2, 2023

janosh merged commit 8ce1cdd into materialsproject:master Nov 2, 2023
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Fix `Atoms.cluster_from_file()` in `io.feff.inputs` giving wrong number of atoms #3426

Fix `Atoms.cluster_from_file()` in `io.feff.inputs` giving wrong number of atoms #3426

kaifengZheng commented Oct 26, 2023

janosh Oct 26, 2023

janosh Oct 26, 2023

kaifengZheng Oct 26, 2023

janosh Oct 27, 2023

janosh Oct 27, 2023

kaifengZheng Oct 27, 2023

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	if line and line[0].__contains__("*"):
	if line and line.startswith("*"):

Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms #3426

Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms #3426

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kaifengZheng commented Oct 26, 2023

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Fix `Atoms.cluster_from_file()` in `io.feff.inputs` giving wrong number of atoms #3426

Fix `Atoms.cluster_from_file()` in `io.feff.inputs` giving wrong number of atoms #3426

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