minor change to avoid warning from ase - #22

Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom
mdforti:master
Open

minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom
mdforti:master

Conversation

@yury-lysogorskiy

@yury-lysogorskiyyury-lysogorskiy commented Nov 22, 2022

Copy link
Copy Markdown
Member

on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:

 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification

@mdforti
minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed the master branch 2 times, most recently from 165dca3 to f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
 minor change to avoid warning from ase - #22
Open
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Open
 minor change to avoid warning from ase#22
yury-lysogorskiy wants to merge 3 commits into
ICAMS:masterfrom 
mdforti:master
Conversation
@yury-lysogorskiy
@yury-lysogorskiyyury-lysogorskiy
commented
Nov 22, 2022

Copy link


Copy Markdown

Member
on my system (fresh install, ase 3.22.1 ) the relevant part of the traceback:
 File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead

which is solved with this modification
@mdforti
 minor change to avoid warning from ase
f2bf2ca
on my system (fresh install, ase 3.22.1 ) the relevant part of the
traceback:
```
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/atoms.py", line 731, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 709, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/calculators/calculator.py", line 737, in get_property
self.calculate(atoms, [name], system_changes)
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/pyace/asecalc.py", line 161, in calculate
if self.atoms.number_of_lattice_vectors == 3:
File "/scratch/AnacondaEnvironments/ml_datasets/lib/python3.9/site-packages/ase/utils/__init__.py", line 62, in deprecated_function
warnings.warn(warning)
FutureWarning: Please use atoms.cell.rank instead
```
which is solved with this modification
@mdforti
mdfortiforce-pushed
the
master
branch
2 times, most recently
from
165dca3 to
f2bf2caCompareDecember 17, 2022 07:56
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

2 participants

@yury-lysogorskiy@mdforti