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   "source": [
    "# $\\text{Preparing } \\textit{ab-initio} \\text{ data}$"
   ]
  },
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   "id": "5d7273cd",
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   "source": [
    "## Displacements using CFOUR\n",
    "\n",
    "To create displaced geometries in `.xyz` format, we will follow these steps:\n",
    "\n",
    "1. **Geometry Optimization and Frequency Calculation**:\n",
    "   - Use **CFOUR** to optimize the molecular geometry and compute harmonic frequencies.\n",
    "   - Extract the results from the `output` file generated by the harmonic frequency calculation.\n",
    "\n",
    "2. **Generating Displacements**:\n",
    "   - Utilize the `cfour_displacements.py` script located in the `Tools` directory to process the output and generate the displaced geometries in `.xyz` format."
   ]
  },
  {
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   "metadata": {},
   "source": [
    "### Configuring and Running the `cfour_displacements.py` Script\n",
    "\n",
    "To generate displaced geometries using the `cfour_displacements.py` script, configure the following variables within the script:\n",
    "\n",
    "```python\n",
    "############## Variables to Change ###############\n",
    "\n",
    "inputfile = \"\"  # Output file from CFOUR frequency calculation\n",
    "natoms = 0      # Number of atoms in the molecule\n",
    "is_linear =   # Indicate whether the molecule is linear (True or false)\n",
    "\n",
    "min_displacement = 0.0  # Minimum displacement in dimensionless units\n",
    "max_displacement = 0.0  # Maximum displacement in dimensionless units\n",
    "step_displacement = 0.0  # Step size for displacement in dimensionless units\n",
    "\n",
    "outputfile = \"\"  # Output directory for the displaced geometries\n",
    "##################################################\n",
    "```"
   ]
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   "source": [
    "After configuring the variables, execute the script using the following command:\n",
    "```bash\n",
    "python3 cfour_displacements.py\n",
    "```\n",
    "\n",
    "### Displaced Geometries\n",
    "Upon executing the `cfour_displacements.py` script, a directory will be created containing all displaced geometries in `.xyz` format. The naming convention for these files is as follows:\n",
    "\n",
    "```\n",
    "geo_v{normal_mode}_{displacement}.xyz\n",
    "```\n",
    "\n",
    "- **`normal_mode`**: Indicates the vibrational normal mode.\n",
    "- **`displacement`**: Specifies the displacement value in dimensionless units, including the sign for negative displacements.\n",
    "\n",
    "For example, `geo_v1_-01.xyz` for a negative displacement and `geo_v1_01.xyz` for a positive displacement."
   ]
  },
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   "cell_type": "markdown",
   "id": "29d3c16b",
   "metadata": {},
   "source": [
    "## Preparing ADCC Input Files\n",
    "\n",
    "### Running ADCC Calculations\n",
    "To process these geometry files and run ADCC calculations, you can use the provided Python script `run_adc.py`. This script takes a single geometry file as input, performs an SCF calculation using pyscf, computes excited states using adcc, and generates a molden file.\n",
    "\n",
    "#### run_adc.py\n",
    "```python\n",
    "import numpy as np\n",
    "import sys\n",
    "import adcc\n",
    "import pyscf\n",
    "from pyscf.tools import molden\n",
    "\n",
    "# Create the molden filename\n",
    "def change_extension(filename):\n",
    "    if filename.endswith('.xyz'):\n",
    "        return filename[:-4] + '.molden'\n",
    "    return filename\n",
    "\n",
    "def main():\n",
    "    # Run SCF in pyscf\n",
    "    mol = pyscf.gto.M(\n",
    "        atom=sys.argv[1],  # Take the geometry from the displaced folder\n",
    "        basis=\"cc-pvdz\"\n",
    "    )\n",
    "\n",
    "    scfres = pyscf.scf.RHF(mol)\n",
    "    scfres.conv_tol = 1e-13\n",
    "    scfres.kernel()\n",
    "\n",
    "    adcc.set_n_threads(8)\n",
    "    hf = adcc.ReferenceState(scfres)\n",
    "    print(adcc.LazyMp(hf).energy(level=3))  # Print MP3 energy; for better precision, CCSD(T) could be used\n",
    "    state = adcc.cvs_adc3(scfres, n_singlets=10, core_orbitals=4)\n",
    "    print(state.describe())  # Print the data obtained\n",
    "    print(state.describe_amplitudes())  # Print the transitions\n",
    "\n",
    "    new_filename = change_extension(sys.argv[1])\n",
    "    # Creating the .molden file\n",
    "    with open(new_filename, 'w') as f1:\n",
    "        molden.header(mol, f1)\n",
    "        molden.orbital_coeff(mol, f1, scfres.mo_coeff, ene=scfres.mo_energy, occ=scfres.mo_occ)\n",
    "\n",
    "if __name__ == \"__main__\":\n",
    "    main()\n",
    "```\n",
    "\n",
    "### Submitting Jobs to the Cluster\n",
    "To run the `run_adc.py` script on a cluster, you can use the following sbatch script. Replace the placeholders (X) with appropriate values for your system.\n",
    "\n",
    "#### run_sbatch_adcc.sh\n",
    "```bash\n",
    "#!/bin/bash\n",
    "#SBATCH --partition=X\n",
    "#SBATCH --nodes=X\n",
    "#SBATCH --ntasks-per-node=X\n",
    "#SBATCH --time=XX:XX:XX\n",
    "#SBATCH --mem=Xgb\n",
    "\n",
    "new_filename=\"${1%.xyz}.out\"  # This will create an output file\n",
    "python3 run_adc.py ${1} > $new_filename\n",
    "```\n",
    "\n",
    "### Running Multiple Calculations\n",
    "To efficiently run calculations for all displaced geometries, you can use the following bash script. This script iterates over all normal modes and displacements, submitting a separate job for each geometry file. Ensure that the filename formatting matches the output of `cfour_displacements.py`.\n",
    "\n",
    "#### run_everything.sh\n",
    "```bash\n",
    "#!/bin/bash\n",
    "nmodes=x\n",
    "min_disp=x\n",
    "max_disp=x\n",
    "step=x\n",
    "for nmode in $(seq 1 1 $nmodes); do\n",
    "    for ((disp=$min_disp; disp<=$max_disp; disp+=$step)); do\n",
    "        if [ $disp -lt 0 ]; then\n",
    "            inpgeo=$(printf \"geo_v%d_%03d.xyz\" $nmode $disp)\n",
    "        else\n",
    "            inpgeo=$(printf \"geo_v%d_%02d.xyz\" $nmode $disp)\n",
    "        fi\n",
    "        sbatch run_sbatch_adcc.sh $inpgeo\n",
    "    done\n",
    "done\n",
    "```\n",
    "\n",
    "**Note**: Adjust the values of `nmodes`, `min_disp`, `max_disp`, and `step` to match your specific calculation parameters. Also, verify that the filename formatting in the script (e.g., `geo_v%d_%03d.xyz` for negative displacements and `geo_v%d_%02d.xyz` for positive displacements) matches the naming convention used by `cfour_displacements.py`. For example, this script assumes filenames like `geo_v1_-01.xyz` and `geo_v1_01.xyz`."
   ]
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   "cell_type": "markdown",
   "id": "17690535",
   "metadata": {},
   "source": [
    "### Extracting Data from ADC Output Files\n",
    "\n",
    ". **Configure the Extraction Script**:\n",
    "   - Open `Tools/extract_adcc.py` in a text editor.\n",
    "   - Modify the configuration parameters as needed\n",
    "   - Running it by executing\n",
    "     ```bash\n",
    "        python3 extract_adcc.py\n",
    "     ```\n",
    "   - This will create the data files `gs_v{mode}.dat` and `ce{state}_v{mode}.dat`, each file consisting of two columns, the displacement and the energy.\n",
    "    "
   ]
  }
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