1. Overview of pysisyphus

pysisyphus is a software-suite for the exploration of potential energy surfaces in ground- and excited states. User input is read from YAML files, but it can also be used as a python library to set up custom workflows.

Below you can find a screencast of the transition state (TS) search for the famous alanine dipeptide isomerization at the xtb level of theory. It starts with pre-optimizations of the initial and final geometry, a subsequent growing string calculation in delocalized internal coordinates to generate a guess for the final TS optimization and with which it concludes.

Besides being able to track excited states over the course of an optimization the idea of pysisyphus is to provide tools for handling the whole process of calculating reaction paths, starting from pre-optimizing the given input geometries for chain of states methods and ending with the hessian calculation on the optimized IRC endpoints.

1.1. Entry points

pysisyphus provides several entry points that can be called from the shell (command line). The available commands of the entry points can be queried with the -h or --help arguments:

# Run calculations (Minima optimization, TS search, IRC, NEB, GS, ...)
pysis
# Plotting of path-energies, optimization progress, IRC progress, etc ...
pysisplot
# Manipulate a .trj file or multiple .xyz files
pysistrj

1.1.1. pysis

Called with a YAML-input file. Simple and more complex examples can be found in the examples directory of this repository. Some common arguments are given below:

usage: pysis [-h] [--clean] --cp CP]
         [yaml]

positional arguments:
    yaml                  Start pysisyphus with input from a YAML file.

optional arguments:
    --clean               Ask for confirmation before cleaning.
    --cp CP, --copy CP    Copy .yaml file and corresponding geometries to a new
                          directory. Similar to TURBOMOLEs cpc command.

1.1.2. pysisplot

Visualization/plotting of the pysisyphus calculations. Some common arguments are given below:

usage: pysisplot (--cosforces | --cosens | --all_energies | --afir | --opt | --irc | --overlaps)

optional arguments:
  --cosforces, --cf    Plot image forces along a COS.
  --cosens, --ce       Plot COS energies.
  --all_energies, -a   Plot ground and excited state energies from 'overlap_data.h5'.
  --afir               Plot AFIR and true -energies and -forces from an AFIR calculation.
  --opt                Plot optimization progress.
  --irc                Plot IRC progress.
  --overlaps, -o

1.1.3. pysistrj

Please see pysistrj --help for a list of available arguments.

1.2. Available calculators

1.2.1. Excited state capabilities

Program	Gradient	Hessian	Exc. states	Version
ORCA	y	y	TD-DFT, TDA	4.2.x
Turbomole	y	y	TD-DFT, TDA, ricc2	7.2-7.4
Gaussian16	y	y	tested TD-DFT, TDA
PySCF	y	y	tested TD-DFT	1.7.5
OpenMOLCAS	y	n	&rasscf	Not yet derived from OverlapCalculator

1.2.2. Ground states capabilities

Program	Gradient	Hessian	Version
MOPAC2016	y	y
XTB	y	y	6.3.2
QCEngine	y	n	>= 0.16.0
Psi4	y	y

1.2.3. Pure python calculators & Wrappers

Program	Gradient	Hessian	Comment
Sympy 2D	y	y	Many analytical potentials (LEPS, Rosenbrock, Cerjan-Miller, Muller-Brown, ...)
Lennard-Jones	y	n	No periodic boundary conditions
AFIR	y	n
ONIOM	y	n	Arbitrary number of layers with multicenter-support in the highest layer.
FakeASE	y	n	Wraps pysisyphus calculators so they can be used with ase.

1.3. Available algorithms

1.3.1. Chain Of States Methods

Algorithm	Coordinates	Comment
Nudged Elastic Band (NEB)	Cartesian, DLC planned	Climbing Image variants, Doubly nudged variant
Adaptive NEB	Cartesian	Not well tested
Free-End NEB	Cartesian	Not well tested
Simple Zero-Temperature-String	Cartesian	Equal spacing, energy-dependent spacing
Growing String Method	Cartesian, DLC

1.3.2. Chain Of States Optimizer

Algorithm	Comment	Links
Steepest Descent	Backtracking variant	NEB-Optimizers
Conjugate Gradient	Backtracking variant	NEB-Optimizers
QuickMin		NEB-Optimizers
FIRE		NEB-Optimizers
BFGS		NEB-Optimizers

1.3.3. Transition state optimization

Algorithm	Comment	Links
RS-P-RFO	default	RFO-Paper, RS-Paper
RS-I-RFO		RFO-Paper, RS-Paper
TRIM		TRIM-Paper
Dimer method

1.3.4. Intrinsic Reaction Coordinate integrators

Algorithm	Comment	Links
Damped-Velocity-Verlet		DVV-Paper
Euler	Not recommended
EulerPC	default	Kaestner-PC, Euler-PC
Gonzales-Schlegel 2		GS2-Paper
Local Quadratic Approximation		LQA-Paper
Modified IMK		IMK-Paper
Runge-Kutta-4	Not recommended

1.4. Additional remarks

pysisyphus uses the tempfile module from the python stdlib. The location of the temporary directories can be controlled by setting the $TMPDIR environment variable before executing pysis.

export TMPDIR=[tmpdir]