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Ice Analog Spectra Generator

The provided scripts generate amorphous solids and manage Gaussian16 density functional theory (DFT) optimization and excited state calculations.
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Table of Contents
  1. About The Project
  2. Getting Started
  3. Usage
  4. Roadmap
  5. Contributing
  6. License
  7. Contact
  8. Acknowledgments

About The Project

Built With

Getting Started

Prerequisites

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.

Usage

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.

buildGeoms jobList Object

{
        "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
}

qmgr jobList Object

{
        "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": ""
          }
        ]
}

qmgr jobList excList object

{
            "excMethod": "CAM-B3LYP",
            "excBasisSet": "6-311G(d)",
            "memComFile": "1600",
            "memPBSFile": "10",
            "nStates": 25,
            "SCRF": ""
}

qmgr jobList vibList object

{
            "excMethod": "CAM-B3LYP",
            "excBasisSet": "6-31G(d)",
            "memComFile": "1600",
            "memPBSFile": "10",
            "SCRF": ""
}

dataAnalysis output plot dft excList object

{
    "dataPath": "data/test2",
    "excMethod": "wB97XD",
    "excBasisSet": "6-31G(d)",
    "nStates": 25,
    "acquiredStates": "25",
    "SCRF": "",
    "line": { "color": "red", "type": "-" }
}

dataAnalysis output plot dft excList object

{
    "path": "exp_data/nh3_gas.csv",
    "units": { "input": "eV", "output": "eV" },
    "line": { "color": "k", "type": "--" },
    "legendLabel": "Test 1"
}

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Roadmap

  • [] Vibrational Spectroscopy Graphs
  • [] Restructure qstat call based on queue type

See the open issues for a full list of proposed features (and known issues).

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Contributing

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!

  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request

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License

Distributed under the MIT License. See LICENSE.txt for more information.

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Contact

Austin Wallace - [email protected]

Project Link: https://github.com/Awallace3/ice_analog_spectra_generator

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Acknowledgments

If you are curious about Neovim check out my nvim repo!

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