The provided scripts generate amorphous solids and manage Gaussian16 density functional theory (DFT) optimization and excited state calculations.
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You will need to install Python3. While earlier versions of python might work, the codebase has been tested for version 3.10.1.
- Python3
python3 --version
Check the requirements.txt file for the versions of the dependencies. A virtual environment is recommended for installing these dependencies and to ensure that the scripts execute correctly.
The intent of this codebase is to enable users to generate amorphous solid datasets with ease. Therefore, the primary user interface will be through the input.json file with an example below. Change the parameters to meet your needs. Note that the '[]' designates arrays while '{}' designates objects.
{
"buildGeoms": {
"enable": false,
"jobList": [
{
"dataPath": "data/test",
"inputCartesianFiles": [
{ "file": "mon_h2o.xyz", "count": 1 },
{ "file": "mon_nh3.xyz", "count": 0 }
],
"clusters": 5,
"boxLength": 3,
"boxGrowth": {
"enable": true,
"increment": 3
},
"minDistanceMolecules": 2,
"optMethod": "B3LYP",
"optBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"startNum": 1
},
{
"dataPath": "data/test2",
"inputCartesianFiles": [
{ "file": "mon_h2o.xyz", "count": 0 },
{ "file": "mon_nh3.xyz", "count": 1 }
],
"clusters": 5,
"boxLength": 3,
"boxGrowth": {
"enable": true,
"increment": 3
},
"minDistanceMolecules": 2,
"optMethod": "B3LYP",
"optBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"startNum": 1
}
]
},
"qmgr": {
"enable": { "exc": false, "vib": false},
"options": {
"minDelay": 1,
"maxResub": 1000,
"maxQueue": 200,
"cluster": "map"
},
"jobList": [
{
"dataPath": "data/test",
"outName": "t1",
"optResub": {
"optMethod": "B3LYP",
"optBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10"
},
"excList": [
{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-311G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"nStates": 25,
"SCRF": ""
}
],
"vibList": [
{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"SCRF": ""
}
]
},
{
"dataPath": "data/test2",
"outName": "t2",
"optResub": {
"optMethod": "B3LYP",
"optBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10"
},
"excList": [
{
"excMethod": "wB97XD",
"excBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"nStates": 25,
"SCRF": ""
}
],
"vibList": [
{
"excMethod": "wB97XD",
"excBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"SCRF": ""
}
]
}
]
},
"dataAnalysis": {
"enable": true,
"dataPath": "data/",
"temperature": 273.15,
"type": "exc",
"output": {
"numerical": {
"enable": true,
"type": ".json",
"outFile": "tmp.json",
"excList": [
{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-311G(d,p)",
"nStates": 25,
"acquiredStates": "25",
"SCRF": ""
},
{
"excMethod": "wB97XD",
"excBasisSet": "6-311G(d,p)",
"nStates": 25,
"acquiredStates": "25",
"SCRF": ""
}
]
},
"plot": {
"enable": true,
"range": { "x": [1, 12], "y": [0, 1.5] },
"x_units": "eV",
"fileName": "data.png",
"title": "",
"dpi": 400,
"dft": {
"legendLabelBasisSet": false,
"peaks": false,
"excList": [
{
"dataPath": "data/test2",
"excMethod": "wB97XD",
"excBasisSet": "6-31G(d)",
"nStates": 25,
"acquiredStates": "25",
"SCRF": "",
"line": { "color": "red", "type": "-" }
}
]
},
"exp": {
"enable": true,
"peaks": false,
"expData": [
{
"path": "exp_data/nh3_gas.csv",
"units": { "input": "eV", "output": "eV" },
"line": { "color": "k", "type": "--" },
"legendLabel": "Test 1"
},
{
"path": "exp_data/nh3_solid.csv",
"units": { "input": "eV", "output": "eV" },
"line": { "color": "b", "type": "-" },
"legendLabel": "Test 2"
}
]
}
}
}
}
}To manage more datasets with a single script running in the background you can copy the objects below for the desired function, edit the parameters, and insert into the correct jobList array in input.json. Remember to add commas after the previous object and that the last object in the array should not have a comma afterwards.
{
"dataPath": "data/test",
"inputCartesianFiles": [
{ "file": "mon_h2o.xyz", "count": 1 },
{ "file": "mon_nh3.xyz", "count": 0 }
],
"clusters": 5,
"boxLength": 3,
"boxGrowth": {
"enable": true,
"increment": 3
},
"minDistanceMolecules": 2,
"optMethod": "B3LYP",
"optBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"startNum": 1
}{
"dataPath": "data/test",
"outName": "t1",
"optResub": {
"optMethod": "B3LYP",
"optBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10"
},
"excList": [
{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-311G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"nStates": 25,
"SCRF": ""
}
],
"vibList": [
{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"SCRF": ""
}
]
}{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-311G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"nStates": 25,
"SCRF": ""
}{
"excMethod": "CAM-B3LYP",
"excBasisSet": "6-31G(d)",
"memComFile": "1600",
"memPBSFile": "10",
"SCRF": ""
}{
"dataPath": "data/test2",
"excMethod": "wB97XD",
"excBasisSet": "6-31G(d)",
"nStates": 25,
"acquiredStates": "25",
"SCRF": "",
"line": { "color": "red", "type": "-" }
}{
"path": "exp_data/nh3_gas.csv",
"units": { "input": "eV", "output": "eV" },
"line": { "color": "k", "type": "--" },
"legendLabel": "Test 1"
}- [] Vibrational Spectroscopy Graphs
- [] Restructure qstat call based on queue type
See the open issues for a full list of proposed features (and known issues).
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!
- Fork the Project
- Create your Feature Branch (
git checkout -b feature/AmazingFeature) - Commit your Changes (
git commit -m 'Add some AmazingFeature') - Push to the Branch (
git push origin feature/AmazingFeature) - Open a Pull Request
Distributed under the MIT License. See LICENSE.txt for more information.
Austin Wallace - austinwallace196@gmail.com
Project Link: https://github.com/Awallace3/ice_analog_spectra_generator
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