Simulate

The Simulate module defines restricted interfaces to computational chemistry codes.

Accuracy Levels

The core concept behind simulation in ExaMol is that there are few levels The idea is to prioritize consistency of settings across computations over flexibility in being able to run slightly-different computations in a workflow.

Each level maps to a different computational chemistry code using a specific set of parameters that are validated for the recipes available through ExaMol.

Name	Interface	Code	Description
xtb	ASESimulator	xTB	Tight binding using the GFN2-xTB parameterization
guassian_[method]_[basis]	ASESimulator	Gaussian	Any method and basis set supported by Gaussian. Replace [method] and [basis] with desired settings
mopac_[method]	ASESimulator	MOPAC	Any method supported by MOPAC. Replace [method] with the lower case method name
cp2k_blyp_[basis]	ASESimulator	CP2K	Gaussian Plane Wave DFT with a BLYP XC function and GTH basis sets. Supports a basis of szv or dzvp for the SZV-MOLOPT-GTH and DZVP-MOLOPT-GTH, respectively.
cp2k_b3lyp_[basis]	ASESimulator	CP2K	Gaussian-Augmented Plane Wave DFT with a B3LYP XC function. Supports a basis of svp or tzvpd for the def2-SVP and def2-TZVPD, respectively.
cp2k_wb97x-d3_[basis]	ASESimulator	CP2K	Gaussian-Augmented Plane Wave DFT with a ωB97x-D3 XC function. Supports a basis of tzvpd for the def2-TZVPD.

After selecting a level of accuracy, select the interface needed to run it.

The Simulator Interface

ExaMol provides workflow-compatible interfaces for common operations in quantum chemistry through the BaseSimulator interface. Each Simulator implementation provides functions to compute the energy of a structure and a function to perform a geometry optimization which take inputs and produce outputs suitable for transmitting between computers.

Create a simulator interface by providing it first with any options needed to run on your specific supercomputer. An interface that will use CP2K could, for example, require a path to the scratch directory and the mpiexec command used to launch it.

sim = ASESimulator(
    scratch_dir='cp2k-files',
    cp2k_command=f'mpiexec -n 8 --ppn 4 --cpu-bind depth --depth 8 -env OMP_NUM_THREADS=8 '
                 '/path/to/exe/local_cuda/cp2k_shell.psmp',
)

The interface can then run the energy computations or optimizations with CP2K. Each computation returns a SimResult object containing the energy and structure of the outputs.

out_res, traj_res, _ = sim.optimize_structure(
    xyz=xyz,
    config_name='cp2k_blyp_dzvp',
    charge=0
)
solv_res, _ = sim.compute_energy(
    xyz=out_res.xyz,
    config_name='cp2k_blyp_dzvp',
    charge=1,
    solvent='acn'
)

Adding New Accuracy Levels

Note

Work in Progress. Logan is working to make this easier (see Issue #40)