pysisyphus

https://pysisyphus.readthedocs.io/en/latest/
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pysisyphus is a software suite for exploring potential energy surfaces in ground and excited states,...
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### Install from Source

Source: https://pysisyphus.readthedocs.io/en/latest/installation.html

Clone the repository and perform an editable installation for development purposes.

```bash
git clone https://github.com/eljost/pysisyphus.git $install_dir
cd $install_dir
# Install with -e if you want an editable installation
python -m pip install [-e] .
# Installation of extras is also possible. 'sphinx' is only needed if you
# want to build the documentation.
# python -m pip install [-e] .[test]
```

```bash
git switch dev
```

--------------------------------

### Install pysisyphus from Source

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/installation.rst.txt

Clone the repository and install pysisyphus from source. Use the '-e' flag for an editable installation, which is useful for development. Extras like 'test' or 'sphinx' can also be installed.

```bash
git clone https://github.com/eljost/pysisyphus.git $install_dir
cd $install_dir
# Install with -e if you want an editable installation
python -m pip install [-e] .
# Installation of extras is also possible. 'sphinx' is only needed if you
# want to build the documentation.
# python -m pip install [-e] .[test]
```

--------------------------------

### Start Interactive Shell

Source: https://pysisyphus.readthedocs.io/en/latest/nix.html

Launch an interactive shell environment with pysisyphus installed.

```bash
nix shell github:eljost/pysisyphus
```

--------------------------------

### YAML Calculator Configuration Example

Source: https://pysisyphus.readthedocs.io/en/latest/calculators.html

Example of a YAML input file demonstrating common keywords for calculator type, resources, and excited-state calculations. Ensure keywords are valid for the chosen calculator.

```yaml
geom:
 [... omitted ...]
calc:
 type: orca                     # Calculator type, e.g. g09/g16/openmolcas/ 
                                # orca/pyscf/turbomole/dftb+/mopac/psi4/xtb

 pal: 1                         # Number of CPU cores
 mem: 1000                      # Memory per core
 charge: 0                      # Charge
 mult: 1                        # Multiplicity
 # Keywords for ES calculations
 track: False                   # Activate ES tracking
 ovlp_type: tden                # Tracking algorithm
 ovlp_with: previous            # Reference cycle selection
 # Additional calculator specific keywords
 [... omitted ...]
opt:
 [... omitted ...]


```

--------------------------------

### Configure Layered Optimization in YAML

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/microiterations.rst.txt

Example configuration for a layered optimization setup using the LayerOpt class.

```yaml
geom:
 type:
  cartesian
 fn: [filename of initial geometry]
calc:
 type:
  oniom:
   ...
opt:
 type:
  layer:
   [layers:
     - # dummy for layer 0 (real system)
```

--------------------------------

### Install via Pip

Source: https://pysisyphus.readthedocs.io/en/latest/installation.html

Install the latest stable release from PyPI or upgrade the pip package manager.

```bash
python -m pip install pysisyphus
# Installation of additional optional dependencies is also possible
# python -m pip install pysisyphus[test]
```

```bash
python -m pip install --upgrade pip
```

--------------------------------

### Install pysisyphus from PyPI

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/installation.rst.txt

Install the latest stable release of pysisyphus using pip. This is the recommended method for users not involved in development. Optional dependencies can be installed with extras.

```bash
python -m pip install pysisyphus
# Installation of additional optional dependencies is also possible
# python -m pip install pysisyphus[test]
```

--------------------------------

### External Potential Configuration (DFTD3 Example)

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/calculators.rst.txt

Example of how to configure an external potential, specifically the D3 dispersion correction, within the pysisyphus input structure.

```APIDOC
## External Potential Configuration Example

### Description
This snippet shows the general input structure for defining external potentials, with a specific example for the D3 dispersion correction.

### Method
N/A (Configuration Example)

### Endpoint
N/A (Configuration Example)

### Parameters
N/A (Configuration Example)

### Request Example
```yaml
calc:
 type: ext
 # Multiple potentials could be specified here as a list
 potentials:
   # Add atom-pairwise D3 dispersion correction as a differentiable, external potential
   - type: d3
     # Functional is specified in TURBOMOLE format, all lower case.
     functional: pbe
     # Optional Becke-Johnson damping, default false, recommended true
     bjdamping: true

calc:
 type: [actual calculator that is wrapped by ExternalPotential]
```

### Response
N/A (Configuration Example)
```

--------------------------------

### ER-Diabatization Example for OMP3

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/diabatization.rst.txt

This example demonstrates ER-diabatization for *trans*-OMP3. It requires setting unlimited stack size and then executing the diabatization command. The calculation involves adiabatic states and detachment-attachment densities.

```shell
#!/bin/bash
ulimit -s unlimited
```

--------------------------------

### Verify pysisyphus Installation with Pytest

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/installation.rst.txt

Executes a series of tests to verify the calculator setup for pysisyphus. Requires pyscf and pytest to be installed.

```bash
pytest -v --pyargs pysisyphus.tests
```

--------------------------------

### Development Setup

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/nix.rst.txt

Clone the repository and enter a development shell for hacking on Pysisyphus.

```bash
git clone https://github.com/eljost/pysisyphus.git && cd pysisyphus
```

```bash
nix develop
```

--------------------------------

### Initialize Shells and Backend

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/shells.html

Handles the setup of integral backends and shell indexing. Requires valid shell objects and ordering parameters.

```python
    backend: Union[str, IntegralBackend] = IntegralBackend.NUMBA_MULTIPOLE,
    ):
        self.shells = shells
        self.ordering = ordering
        self.screen = screen

        # Start integral backend setup
        try:
            self.backend = IntegralBackend(backend)
        # ValueError is raised when backend is a string, not an Enum
        except ValueError:
            self.backend = IntegralBackend[backend.upper()]

        # Only ever import (and compile) numba backend when actually requested,
        # as the compilation/setup takes quite some time.
        if self.backend == IntegralBackend.NUMBA:
            try:
                from pysisyphus.wavefunction import backend_numba

                _backend_modules[IntegralBackend.NUMBA] = backend_numba
            except ModuleNotFoundError:
                print(
                    "numba integral backend was requested but numba package is "
                    "not installed!.\n Falling back to python backend."
                )
                self.backend = IntegralBackend.PYTHON
        elif self.backend == IntegralBackend.NUMBA_MULTIPOLE:
            try:
                from pysisyphus.wavefunction import backend_numba_multipole

                _backend_modules[IntegralBackend.NUMBA_MULTIPOLE] = (
                    backend_numba_multipole
                )
            except ModuleNotFoundError:
                print(
                    "numba integral backend was requested but numba package is "
                    "not installed!.\n Falling back to python backend."
                )
                self.backend = IntegralBackend.PYTHON

        # Pick the actual backend module
        self.backend_module = _backend_modules[self.backend]
        # End integral backend setup

        """
        'native' refers to the original ordering, as used in the QC program. The
        ordering will be reflected in the MO coefficient ordering. With 'native'
        the integrals calculated by pysisyphus must be reorderd, to match the native
        ordering of the MO coefficients.
        """
        assert ordering in ("pysis", "native")

        # Now that we have all Shell objects, we can set their starting indices
        shell_index = 0
        index = 0
        sph_index = 0
        for shell in self.shells:
            shell.shell_index = shell_index
            shell.index = index
            shell.sph_index = sph_index

            shell_index += 1
            # TODO: rename to cart_index
            index += shell.size
            sph_index += shell.sph_size

        # Try to construct Cartesian permutation matrix from cart_order, if defined.
        self._P_cart = None
        self._P_sph = None
        try:
            self.cart_Ps = permut_for_order(self.cart_order)
        except AttributeError:
            pass

        self.atoms, self.coords3d = self.atoms_coords3d
        # Precontract & store coefficients for reordering spherical basis functions
        # and converting them from Cartesian basis functions.
        self.reorder_c2s_coeffs = self.P_sph @ self.cart2sph_coeffs

        self._numba_shells = None
        self._numba_shellstructs = None
```

--------------------------------

### Get Zimmerman Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves data for the Zimmerman benchmark. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_zimmerman_data()
```

--------------------------------

### Get Baker Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves data for the Baker benchmark. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_baker_data()
```

--------------------------------

### Get S22 Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves data for the S22 benchmark dataset. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_s22_data()
```

--------------------------------

### Initialize Infrastructure Parameters

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/io/mol2.html

Configures the infrastructure object using a dictionary of parameters and rendering options.

```python
        charge_type=d["charge_type"],
        atoms_xyzs=d["atoms_xyzs"],
        bonds=d["bond"],
        render_xyz=render_xyz,
    )
    return rendered
```

--------------------------------

### Get XTB RX Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves data for the XTB RX benchmark. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_xtb_rx_data()
```

--------------------------------

### Run Generation Process

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/gen_ints.html

Main entry point for setting up the environment and initiating integral generation.

```python
[docs]
def run():
    args = parse_args(sys.argv[1:])

    l_max = args.lmax
    l_aux_max = args.lauxmax
    out_dir = Path(args.out_dir if not args.write else ".")
    keys = args.keys
    if keys is None:
        keys = list()
    try:
        os.mkdir(out_dir)
    except FileExistsError:
        pass

    try:
        global CART2SPH
        CART2SPH = cart2sph_coeffs(max(l_max, l_aux_max), zero_small=True)
    except NameError:
        print("cart2sph_coeffs import is deactivated or pysisyphus is not installed.")

    # Cartesian basis function centers A and B.
    center_A = get_center("A")
    center_B = get_center("B")
    center_C = get_center("C")
    center_D = get_center("D")
    # center_R = get_center("R")
    Xa, Ya, Za = symbols("Xa Ya Za")

    # Orbital exponents a, b, c, d.
    a, b, c, d = symbols("a b c d", real=True)

    # These maps will be used to convert {Ax, Ay, ...} to array quantities
    # in the generated code. This way an iterable/np.ndarray can be used as
    # function argument instead of (Ax, Ay, Az, Bx, By, Bz).
    A, A_map = get_map("A", center_A)
    B, B_map = get_map("B", center_B)
    C, C_map = get_map("C", center_C)
    D, D_map = get_map("D", center_D)

    boys_import = ("from pysisyphus.wavefunction.ints.boys import boys",)

    #################
    # Cartesian GTO #
    #################

    def cart_gto():
        def cart_gto_doc_func(L_tot):
            (La_tot,) = L_tot
```

--------------------------------

### Get Birkholz RX Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves data for the Birkholz RX benchmark. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_birkholz_rx_data()
```

--------------------------------

### Get Baker TS Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves time-series data for the Baker benchmark. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_baker_ts_data()
```

--------------------------------

### Execute main function

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/ints/boys.html

Standard entry point for running the script.

```python
if __name__ == "__main__":
    run()
```

--------------------------------

### pysisyphus.intcoords.setup_fast Module Functions

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.intcoords.html

Fast methods for finding geometric relationships and setting up internal coordinates.

```APIDOC
## pysisyphus.intcoords.setup_fast.find_bends

### Description
Finds bend internal coordinates within a 3D coordinate set.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_coords3d_** (type) - Description
- **_bonds_** (type) - Description
- **_min_deg_** (type) - Description
- **_max_deg_** (type) - Description
- **_logger =None_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.find_bonds

### Description
Finds bond internal coordinates based on atomic information and distances.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_atoms_** (type) - Description
- **_coords3d_** (type) - Description
- **_covalent_radii =None_** (type) - Description
- **_bond_factor =1.3_** (type) - Description
- **_min_dist =0.1_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.find_bonds_bends

### Description
Finds both bond and bend internal coordinates for a given geometry.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_geom_** (type) - Description
- **_bond_factor =1.3_** (type) - Description
- **_min_deg =15_** (type) - Description
- **_max_deg =175_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.find_bonds_for_geom

### Description
Finds bond internal coordinates specifically for a given geometry.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_geom_** (type) - Description
- **_bond_factor =1.3_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.find_dihedrals

### Description
Finds dihedral internal coordinates within a 3D coordinate set, given existing bonds and bends.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_coords3d_** (type) - Description
- **_bonds_** (type) - Description
- **_bends_** (type) - Description
- **_max_deg_** (type) - Description
- **_logger =None_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.get_bend_candidates

### Description
Generates candidate bend internal coordinates from a list of bonds. Note that this function yields duplicates, e.g., [a, b, c] and [c, b, a].

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_bonds_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.get_bond_vec_getter

### Description
Retrieves a function to get bond vectors, optimized for internal coordinate calculations.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_atoms_** (type) - Description
- **_covalent_radii_** (type) - Description
- **_bonds_for_inds_** (type) - Description
- **_no_bonds_with =None_** (type) - Description
- **_bond_factor =1.3_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup_fast.get_max_bond_dists

### Description
Calculates the maximum possible bond distances based on atomic radii and a bond factor.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_atoms_** (type) - Description
- **_bond_factor_** (type) - Description
- **_covalent_radii =None_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

--------------------------------

### Get Precon Pos Rot Data

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.benchmarks.html

Retrieves data for the Precon Pos Rot benchmark. Requires no specific setup.

```python
pysisyphus.benchmarks.data.get_precon_pos_rot_data()
```

--------------------------------

### Initialize Constraints and Thermostat

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/dynamics/driver.html

Sets up constraints and thermostatting for molecular dynamics. Handles fixed degrees of freedom and prepares the RATTLE closure if constraints are active.

```python
if constraint_kwargs is None:
        constraint_kwargs = dict()

    # Fixed degrees of freedom
    fixed_dof = 0
    if remove_com_v:
        print("Removing center-of-mass velocity.")
        fixed_dof += 3
    constrained_md = constraints is not None
    # Get RATTLE function from closure for constrained MD
    if constrained_md:
        fixed_dof += len(constraints)
        rattle = rattle_closure(
            geom,
            constraints,
            dt,
            energy_forces_getter=energy_forces_getter,
            **constraint_kwargs,
        )
    print(f"Fixed degrees of freedom: {fixed_dof}")
    dof = len(geom.coords) - fixed_dof

    if thermostat is not None:
        sigma = kinetic_energy_for_temperature(len(geom.atoms), T, fixed_dof=fixed_dof)
        thermo_func = THERMOSTATS[thermostat](sigma, dof, dt=dt, tau=timecon)
```

--------------------------------

### Prepare directory and write input

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/calculators/Calculator.html

Prepares a directory and writes the provided input string to the calculator's input file.

```python
if not self.path_already_prepared:
    path = self.prepare_path()
else:
    path = self.path_already_prepared

# Calculators like Turbomole got no input.
if inp:
    inp_path = path / self.inp_fn
    with open(inp_path, "w") as handle:
        handle.write(inp)

return path
```

--------------------------------

### Instanton Class Initialization

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.irc.html

Initializes an Instanton object with images, a calculator getter, and temperature.

```APIDOC
## Instanton Class Initialization

### Description
Creates a new instance of the Instanton class to represent a periodic path.

### Parameters
- **images** (list) - Required - List of molecular images.
- **calc_getter** (callable) - Required - Function to retrieve the calculator.
- **T** (float) - Required - Temperature for the instanton calculation.
```

--------------------------------

### prepare

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/calculators/Calculator.html

Prepares a temporary directory and writes the provided input string to a file within that directory.

```APIDOC
## POST /prepare

### Description
Prepare a temporary directory and write input.
Similar to prepare_path, but the input is also written into the prepared directory.

### Method
POST

### Endpoint
/prepare

### Parameters
#### Query Parameters
- **inp** (str) - Required - Input to be written into the file ``self.inp_fn`` in the prepared directory.

### Response
#### Success Response (200)
- **path** (Path) - Prepared directory.

### Request Example
```json
{
  "inp": "This is the input content."
}
```

### Response Example
```json
{
  "path": "/tmp/pysisyphus_001_abcdef123456"
}
```
```

--------------------------------

### Z-Matrix Example

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/coordinate_systems.rst.txt

Example of a Z-matrix format for defining molecular geometry. Indexing is 1-based, and variable substitution is not supported.

```text
C
N 1 1.35
H 1 1.0 2 105.0
H 2 1.4 1 105.0 3 150.0
H 2 1.4 1 110.0 3 -160.0
```

--------------------------------

### pysisyphus.intcoords.setup Functions

Source: https://pysisyphus.readthedocs.io/en/latest/api/pysisyphus.intcoords.html

Functions for setting up internal coordinates from geometric data.

```APIDOC
## pysisyphus.intcoords.setup.setup_redundant_from_geom

### Description
Sets up redundant internal coordinates from a given geometry.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_geom_** (type) - Description
- **_* args_** (type) - Description
- **_** kwargs_** (type) - Description

### Request Example
(Not applicable)

### Response
(Not specified)
```

```APIDOC
## pysisyphus.intcoords.setup.sort_by_prim_type

### Description
Sorts internal coordinate primitives by their type.

### Method
(Not specified, likely a function call)

### Endpoint
(Not applicable, this is a Python function)

### Parameters
- **_to_sort =None_** (type) - The list of primitives to sort.

### Request Example
(Not applicable)

### Response
(Not specified)
```

--------------------------------

### Upgrade pip

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/installation.rst.txt

Ensure you have a recent version of pip installed to avoid potential issues during package installation. Run this command to upgrade pip.

```bash
python -m pip install --upgrade pip
```

--------------------------------

### Configure Binary Cache

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/nix.rst.txt

Use Cachix to fetch pre-built quantum chemistry codes and reduce build times.

```bash
nix run nixpkgs#cachix use pysisyphus
```

--------------------------------

### YAML Configuration for RFOptimizer

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/min_optimization.rst.txt

Example YAML input for the RFOptimizer, illustrating key parameters for controlling optimization cycles, convergence, Hessian calculation, and line searches.

```yaml
opt:
 type: rfo                      # Optimization algorithm
 max_cycles: 50                 # Maximum number of optimization cycles

 overachieve_factor: 2          # Indicate convergence, regardless of the 
                                    # proposed step when max(grad) and rms(grad)
                                    # are overachieved by factor [n]

 do_hess: True                  # Calculate the hessian at the final geometry
                                    # after the optimization.

 #hessian_recalc: None          # Recalculate exact hessian every n-th cylce

 #hessian_recalc_adapt: None    # Expects a float. Recalculate exact hessian
                                    # whenever the gradient norms drops below
                                    # 1/[n] of the gradient norm at the last hessian
                                    # recalculation.

 #hessian_init: fischer         # Type of model hessian. Other options are: 'calc,
                                    # simple, xtb, lindh, swart, unit'

 #hessian_update: bfgs          # Hessian-update. Other options are: 'flowchart,
                                    # damped_bfgs, bofill'. bofill is not recommended
                                    # for minimum searches.
 #small_eigval_thresh: 1e-8     # Neglect eigenvalues and corresponding eigenvectors
                                    # below this threshold.

 #max_micro_cycles: 50          # No. of micro cycles for the RS-variants. Does not apply
                                    # to TRIM.

 #trust_radius: 0.3             # Initial trust radius.
 #trust_max: 1.0                # Max. trust radius
 #trust_min: 0.1                # Min. trust radius

 #line_search: True             # Do line search

 #gdiis_thresh: 0.0025          # May do GDIIS if rms(step) falls below this threshold
 #gediis_thresh: 0.01           # May do GEDIIS if rms(grad) falls below this threshold

```

--------------------------------

### Get 2-Center 2-Electron Integrals (Spherical)

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/shells.html

A convenience method to get 2-center 2-electron integrals in spherical coordinates by calling `get_1el_ints_sph` with the appropriate key.

```python
def get_2c2el_ints_sph(self):
        return self.get_1el_ints_sph("int2c2e")
```

--------------------------------

### Get 2-Center 2-Electron Integrals (Cartesian)

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/shells.html

A convenience method to get 2-center 2-electron integrals in Cartesian coordinates by calling `get_1el_ints_cart` with the appropriate key.

```python
def get_2c2el_ints_cart(self):
        return self.get_1el_ints_cart("int2c2e")
```

--------------------------------

### Inline XYZ Input Example

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/coordinate_systems.rst.txt

Example of inline coordinate input for XYZ format using the 'redund' coordinate system type. Ensure proper indentation.

```yaml
geom:
 type: redund
 fn: |
  2

  H 0.0 0.0 0.0
  H 0.0 0.0 0.7
```

--------------------------------

### Initialize Integral Backend Modules

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/shells.html

Sets up a dictionary mapping IntegralBackend enum values to their corresponding Python modules.

```python
IntegralBackend = Enum("IntegralBackend", ["PYTHON", "NUMBA", "NUMBA_MULTIPOLE"])
_backend_modules = {
    IntegralBackend.PYTHON: backend_python,
}
```

--------------------------------

### Obtain Development Shell

Source: https://pysisyphus.readthedocs.io/en/latest/nix.html

Enter a development environment configured for pysisyphus.

```bash
nix develop
```

--------------------------------

### Configure ONIOM2 optimization with native implementation

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/microiterations.rst.txt

Example configuration for an ONIOM2 optimization of Hexaphenylethane using the native pysisyphus ONIOM calculator.

```yaml
- geom:
   type:
    cartesian:
  opt:
   type:
    lbfgs:
      ]
```

--------------------------------

### Example Usage of generate_wilson

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/intcoords/generate_derivatives.html

Demonstrates how to call the `generate_wilson` function to create derivative files. It shows two examples: one using standard math and another using mpmath for higher precision.

```python
if __name__ == "__main__":
    generate_wilson(out_fn="derivatives.py", use_mpmath=False)
    # print()
    generate_wilson(out_fn="mp_derivatives.py", use_mpmath=True)
    # generate_wilson(out_fn="lindisp.py", use_mpmath=False)
```

--------------------------------

### Instanton Class Initialization

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/irc/Instanton.html

Initializes the Instanton class with images, a calculator getter, and temperature. Pre-calculates action prefactors and indices.

```python
import numpy as np
import scipy as sp

from pysisyphus.Geometry import Geometry

class Instanton:
    def __init__(self, images, calc_getter, T):
        self.images = images
        self.calc_getter = calc_getter
        for image in self.images:
            image.set_calculator(calc_getter())
        self.T = T

        # Pre-calculate action prefactors for the given temperature
        beta = 1 / (sp.constants.Boltzmann * self.T)  # Joule
        beta_hbar = beta * sp.constants.hbar  # seconds
        beta_hbar_fs = beta_hbar * 1e15  # fs
        self.beta_hbar = beta_hbar_fs
        self.P_over_beta_hbar = self.P / self.beta_hbar
        self.P_bh = self.P_over_beta_hbar
        """The Instanton is periodic: the first image is connected to the
        last image.

        At k=0 the index k-1 will be -1, which points to the last image.

        Below we pre-calculate some indices (assuming N images).
            unshifted indices ks: k = {0, 1, .. , N-1}
            shifted indices ksm1: k-1 = {-1, 0, 1, .. , N-2}
            shifted indices ksp1: k+1 = {1, 2, .. , N-1, 0}
        """
        self.ks = np.arange(self.P)
        self.ksm1 = self.ks - 1
        self.ksp1 = self.ks + 1
        self.ksp1[-1] = 0  # k+1 for the last image points to the first image

        self.coord_type = "mwcartesian"
        self.internal = None

    @property
    def P(self):
        return len(self.images)
```

--------------------------------

### GET /V

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/wavefunction/wavefunction.html

Retrieves 1-electron Coulomb integrals.

```APIDOC
## GET /V

### Description
Calculates 1-electron Coulomb integrals based on provided 3D coordinates and charges.

### Method
GET

### Parameters
#### Query Parameters
- **coords3d** (array) - Required - 3D coordinates of the system.
- **charges** (array) - Required - Charges associated with the coordinates.
```

--------------------------------

### Initialize Wigner Sampler

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/dynamics/wigner.html

Sets up a sampler function for Wigner sampling based on molecular geometry, masses, and Hessian matrix.

```python
@functools.singledispatch
def get_wigner_sampler(
    atoms,
    coords3d: np.ndarray,
    masses: np.ndarray,
    hessian: np.ndarray,
    temperature: float = 0.0,
    nu_thresh: float = 0.0,
    stddevs: float = 6.0,
    seed: Optional[int] = None,
) -> tuple[Callable, int]:
    assert coords3d.shape == (len(masses), 3)
    assert hessian.shape == (coords3d.size, coords3d.size)

    if seed is None:
        seed = secrets.randbits(128)
    rng = np.random.default_rng(seed)

    tmp_geom = Geometry(atoms, coords3d)
    tmp_geom.masses = masses
    tmp_geom.cart_hessian = hessian
    # nus, eigvals, mw_cart_displs (v), cart_displs
    nus, _, v, _ = tmp_geom.get_normal_modes()
    nnus = len(nus)  # Number of non-zero wavenumbers

    imag_nus = nus <= nu_thresh
    nimag_nus = imag_nus.sum()
    use_nu_inds = np.arange(nnus)[~imag_nus]
    if nimag_nus:
        warnings.warn(
            f"Detected {nimag_nus} imaginary wavenumber(s)! They will be ignored in the sampling."
        )

    # Square root of angular frequencies in atomic units. Required to convert the
    # dimensionless Q and P values into atomic units.
    ang_freqs_au_sqrt = np.sqrt(nus * NU2ANGFREQAU)
    ang_freqs_au_sqrt[imag_nus] = 1.0

    span = 2 * stddevs
    # Pre-calculate some of the Laguerre polynomials
    # We use some shortcuts for n == 0 and n == 1
    laguerres = {
        0: lambda _: 1.0,
        1: lambda x: 1.0 - x,
    }

    def get_laguerre(n):
        lag_coeffs = np.zeros(n + 1)
        lag_coeffs[n] = 1.0
        return Laguerre(lag_coeffs)

    # Precompute some often accessed Laguere polynomials
    for i in range(2, 11):
        laguerres[i] = get_laguerre(i)

    mm_sqrt_au = np.sqrt(tmp_geom.masses_rep * AMU2AU)
    M_inv_au = np.diag(1 / mm_sqrt_au)

    def sampler() -> WignerSample:
        qs_nodim = np.zeros(nnus)
        ps_nodim = np.zeros(nnus)
        # Modes that are ignored will not be part of 'use_nu_inds' and their associated
        # sampled normal coordinates and momenta will stay at 0.0 throughout.
        for i in use_nu_inds:
            n = get_vib_state(nus[i], rng, temperature=temperature)
            try:
                lag = laguerres[n]
            except KeyError:
                lag = get_laguerre(n)
                laguerres[n] = lag
            # According to eq. (31) in [3], the absolute value of the Wigner function is
```

--------------------------------

### Initialize batch calculation function

Source: https://pysisyphus.readthedocs.io/en/latest/_modules/pysisyphus/marcus_dim/fit.html

Sets up the environment and partial functions required for batch property calculations.

```python
def get_batch_calc_func(
    geom,
    calc_getter: Callable,
    property: mdtypes.Property,
    fragments: List[Tuple[int]],
    scheduler,
    cart_displs: np.ndarray,
    temperature: float,
    seed=None,
    out_dir=Path("."),
):
    assert temperature >= 0.0, f"{temperature=} must be positive!"

    # Dump fragments
    fragments_trj = "\n".join(
        get_fragment_xyzs(geom, fragments, with_geom=True, with_dummies=True)
    )
    fragment_trj_fn = "fragments.trj"
    with open(out_dir / fragment_trj_fn, "w") as handle:
        handle.write(fragments_trj)
    print(f"Wrote fragments to '{fragment_trj_fn}'")

    property_funcs = {
        property.EPOS_IAO: epos_property_iao,
        property.EPOS_MULLIKEN: epos_property_mulliken,
        property.EEXC: en_exc_property,
    }
    property_func = property_funcs[property]

    try:
        charge = geom.calculator.charge
        mult = geom.calculator.mult
    except AttributeError:
        charge = None
        mult = None

    if (charge is not None) and (mult is not None):
        print(f"       Charge: {charge}")
        print(f" Multiplicity: {mult}")
    print(f"  Temperature: {temperature:.2f} K")
    print(f"     Property: {property}")

    # Calculate wavefunction at equilibrium geometry
    print("Starting calculation at equilibrium geometry")
    # TODO: figure out why this is even needed here ... probably because the calculations aren't done
    # inside the property function(s).
    gs_energy_eq, *_ = geom.all_energies
    # TODO: using 'geom.calc_wavefunction()' leads to a pickling-error later on
    prop_eq = property_func(geom, fragments)
    print("Finished calculation at equilibrium geometry")
    eq_results = {"property_eq": prop_eq, "gs_energy_eq": gs_energy_eq}

    client, pal, calc_msg = setup_calc_client(geom, scheduler)
    print(calc_msg)

    calculate_property_wrapped = functools.partial(
        calculate_property,
        geom=geom,
        calc_getter=calc_getter,
        pal=pal,
        fragments=fragments,
        prop_eq=prop_eq,
        property_func=property_func,
    )
    # Function that create displaced geometries by drawing from a Wigner distribution
    wigner_sampler, seed = get_wigner_sampler(geom, temperature=temperature, seed=seed)
    sampler_wrapped = functools.partial(
        get_displaced_coordinates,
        wigner_sampler=wigner_sampler,
        cart_displs=cart_displs,
```

--------------------------------

### Plotting

Source: https://pysisyphus.readthedocs.io/en/latest/index.html

Examples and functionalities for plotting various calculation results.

```APIDOC
## Plotting

### Description
This section provides examples and guidance on visualizing the results of different types of calculations.

### Examples
- Diels-Alder reaction
  - Plotting optimization progress
  - Plotting COS optimization progress
  - Plotting TS-optimization progress
  - Plotting the Intrinsic Reaction Coordinate
- AFIR
- Excited State Tracking
```

--------------------------------

### Configure Growing String Method (GSM) Optimization

Source: https://pysisyphus.readthedocs.io/en/latest/_sources/chainofstates.rst.txt

Example YAML input for setting up a Growing String Method optimization with specific node and climbing image parameters.

```yaml
precontr:                                # Preconditioning of translation & rotation
preopt:                                  # Preoptimize inital and final geometry
cos:
 type: gs                                # Do a growing string
 max_nodes: 9                            # Total string will have 9 + 2 == 11 images
 climb: False                            # Enable climbing image (CI), usually a good idea.
 climb_rms: 0.005                        # rms(forces) threshold for enabling CI
 climb_lanczos: False                    # Use tangent obtained from Lanczos algorithm for CI.
 climb_lanczos_rms: 0.005                # rms(forces) threshold for enabling Lanczos algorithm.
 reparam_check: rms                      # Criterian for growing new frontier nodes (rms/norm).
 perp_thresh: 0.05                       # Threshold for growing new frontier nodes.
 reparam_every: 2                        # Reparametrize every n-th cycle when NOT fully grown.
 reparam_every_full: 3                   # Reparametrize every n-th cycle when fully grown.
```
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