Dihedral scanner with wavefront propagation
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Python >= 3.6
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Numpy
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geomeTRIC molecule.py, also to enable the
geometric-optimizecommand -
cctools.work_queue [Optional] (to enable the distributed computing feature)
python setup.py install
torsiondrive-launch <InputFile> <Dihedrals.txt> --init_coords <init_coords.xyz> -g <grid_spacing> -e <Engine> (--native_opt) (--wq_port XXX) (-v) > scan.log
torsiondrive-api current_state.json
<InputFile>: An Psi4, QChem or Terachem input file, servering as a template for constrained optimizations.
<Dihedrals.txt>: A txt file containing the definition of dihedral angles, each as 4 atom indices in one line. The number of dihedrals determines the dimension of the scanned grid.
--init_coords <init_coords.xyz>: File contains a trajectory of initial coordinates. Will be mapped to the closest grid point at beginning, replacing the geometry in <InputFile>.
-g <grid_spacing>: Integer number, divisor of 360, angle in degree between each grid point.
-e <Engine>: One of psi4, qchem, terachem
--native_opt: Flag, use quantum software's internal optimizer instead of geomeTRIC optimizer.
--wq_port XXX: Flag, use cctools.work_queue tool to distribute the calculations.
-v: Flag, turn on verbose printing, including the colorful status map :)
The DihedralScanner Class works together with the QMEngine Class, both can be imported and incorporated into other python scripts, to enable more features, and automated scanning for multiple molecules.
Project based on the Computational Chemistry Python Cookiecutter
The development of this code has been supported in part by the following grants and awards:
NIH Grant R01 AI130684-02
ACS-PRF 58158-DNI6