ASE scripts

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Qiang Zhu edited this page Jun 3, 2021 · 9 revisions

ASE provides very convenient tool to manipulate the structures and convert them to different file formats.

Supercell

Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.

fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')

ASE could handle almost all file format in the major codes.

For more information, please visit the following link: https://wiki.fysik.dtu.dk/ase/ase/io/io.html

A more complicated case

Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell. Below is an example of doing so.

fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')

Modify the orientation of surface structure

$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips: Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.

Computing clusters

Scientific topics

Resources

Clone this wiki locally

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
ASE scripts
Jump to bottom

Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally

, '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");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
ASE scripts
Jump to bottom

Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally

, '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
ASE scripts
Jump to bottom

Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally

, '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
ASE scripts
Jump to bottom

Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally

, '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
ASE scripts
Jump to bottom

Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally

, '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('^' + ".*" + '

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ASE scripts
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Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally

, '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
ASE scripts
Jump to bottom

Qiang Zhu edited this page Jun 3, 2021
·
9 revisions
ASE provides very convenient tool to manipulate the structures and convert them to different file formats.
Supercell
Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.
fromase.ioimportread, writestruc=read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')
ASE could handle almost all file format in the major codes.
For more information, please visit the following link:
https://wiki.fysik.dtu.dk/ase/ase/io/io.html
A more complicated case
Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell.
Below is an example of doing so.
fromase.ioimportread, writefromaseimportgeometryfromase.build.supercellsimportmake_supercellimportnumpyasnp#Read structure from POSCAR, this is ase.atom objectstruc=read('gra.vasp',format='vasp')
#make supercell hereP=np.array([[1,-1,0],[1,1,0],[0,0,1]])*2gra1=make_supercell(struc, P)
#After the lattice transformation#the supercell might have unpleasant shape such as #[ 0, -1, 0]#[ 1, 0, 0]#[ 0, 0, 1]#let's apply another transformation herecell_par=gra1.get_cell_lengths_and_angles()
pos1=gra1.get_scaled_positions()
cell1=geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)
#output in any format whichever you wantwrite('POSCAR',gra1, format='vasp')
Modify the orientation of surface structure
$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000 0.000000000000000 0.000000000000000
11.47575000000000 19.87658205495854 0.000000000000000
17.78942000000002 10.27072642572731 29.05000121337461
Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

fromase.ioimportreadfromase.build.supercellsimportmake_supercellimportnumpyasnpat=read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P=np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1=make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)
[22.9515 22.9515 35.57884 60. 60. 60. ]
[22.9515 39.75316411 29.05760871 88.68889365 90. 90. ]

Tips:
Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.
Computing clusters
Scientific topics
Resources
Clone this wiki locally