BranchesTags

Repository files navigation

Python Organic Crystal Simulation Environment (PYOCSE)

This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:

  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)

Python Setup

git clone this repository and then go to the root directory

conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment

conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:

make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples

  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)

You can check the details in misc/uniaxial.py

Contacts:

About

Python Organic Crystal Simulation Environment

Resources

Readme
MIT license
Activity
Custom properties

Stars

3 stars

Watchers

1 watching

Forks

2 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Python Organic Crystal Simulation Environment (PYOCSE)
This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:
  1. Automate the geneation of structural model and force field (through ambertools or openff)
  2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)
Python Setup
git clone this repository and then go to the root directory
conda env create -n pyocse
conda activate pyocse
pip install .

If you want to update the existing ocse enviroment
conda activate pyocse
conda env update --file environment.yml

LAMMPS Setup:
make yes-MOLECULE
make yes-EXTRA-MOLECULE make yes-KSPACE make mpi -j 12

Examples
  1. Add your structure to the database
# Find your structure from https://www.ccdc.cam.ac.uk/structures/Search?tag= {
"csd_code": 'ACSALA',
"ccdc_number": 1101020,
"smiles": "CC(=O)OC1=CC=CC=C1C(O)=O",
}
# Load the pyxtal structurefrompyxtalimportpyxtalxtal=pyxtal(molecular=True)
xtal.from_seed(str(tag['ccdc_number'])+'.cif',
molecules=[str(tag['smiles'])+'.smi'])
xtal.tag=tagprint(xtal)
# Deposit your structurefrompyxtal.dbimportmake_entry_from_pyxtal, databaseentry=make_entry_from_pyxtal(xtal)
db=database('dataset/mech.db')
db.add(entry)
  1. 3D periodic boundary condictions (shearing/tensile/compression)
frompyocse.buildimportBuilderfrompyxtal.dbimportdatabaseimportnumpyasnpimportos# Set the crystal modeldata= [
('ACSALA', [[1,0,0], [0,1,0], [0,0,1]]),
]
style='openff'#'gaff'db=database('dataset/mech.db')
# Define your desired dimension dim= [100, 40, 40]
# Prepare the lammps input filesfordindata:
(code, matrix) =dmatrix=np.array(matrix)
print(code)
xtal=db.get_pyxtal(code)
smiles= [mol.smileformolinxtal.molecules]
bu=Builder(smiles=smiles, style=style)
bu.set_xtal(xtal, para_min=10.0)
# Directoryfolder=code+'-'+styleifnotos.path.exists(folder): os.makedirs(folder)
cwd=os.getcwd()
os.chdir(folder)
# Example 1: tensile, assuming z directiontask1= {'type': 'tensile',
'temperature': 300,
'pressure': 1.0,
'max_strain': 0.1,
'rate': 1e+8,
}
bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dim=dim)
print('Supercell: ', bu.ase_slab.get_cell_lengths_and_angles())
bu.set_task(task1)
bu.lammps_slab.write_lammps()
# Just for a quick view from VESTAbu.ase_slab.write('test.xyz', format='extxyz')
os.chdir(cwd)
You can check the details in misc/uniaxial.py
Contacts:
About
Python Organic Crystal Simulation Environment
Resources
Readme
MIT license
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Used by
Contributors
Languages