Name of the Program: Pilgrim
Program Version : 2021.5
Program Version Date: Nov 22, 2021
Manual Version Date: Nov 22, 2021Pilgrim is an user-friendly program written in Python 3. It was designed to use direct-dynamics to calculate thermal rate constants of chemical reactions and to simulate chemical kinetics mechanisms.
For reaction processes with many elementary steps, each of these steps can be calculated using conventional transition state theory (TST) or variational transition state theory (VTST). In this version, Pilgrim can calculate thermal rate constants with the canonical version of the variational transition state theory (CVT), which requires the calculation of the minimum energy path (MEP) associated to each elementary step. Moreover, multi-dimensional quantum effects can be incorporated through the small-curvature tunneling approximation (SCT). The above methodologies are available for reactions involving a single structure and for reactions involving flexible molecules with multiple conformations. Specifically, for systems with many conformers the program can evaluate each of the elementary reactions by multi-path canonical variational transition state theory (MP-CVT) or multi-structural VTST (MS-VTST). Torsional anharmonicity can be also incorporated through the MSTor and Q2DTor programs.
Pilgrim also performs dual-level calculations automatically. First, low-level calculations are carried out for the reaction of interest and second, single-point energy calculations of the reactants, transition state, points along the MEP and products are performed at a higher level. The low-level calculations are corrected with the high-level single point energies using the interpolated single-point energies (ISPE) algorithm.
Once all the rate constants of the chemical processes of interest are known, by means of their calculation using Pilgrim or by using an analytical expression, it is possible to simulate the whole process using kinetic Monte Carlo (KMC). This algorithm allows performing a kinetics simulation and monitoring the evolution of each chemical species with time, as well as providing its chemical yield.
D. Ferro-Costas, D. G. Truhlar, A. Fernández-Ramos, Pilgrim - version 2021.5 (University of Minneapolis, Minnesota, MN, and Universidade de Santiago de Compostela, Spain, 2021). https://github.com/cathedralpkg/Pilgrim
D. Ferro-Costas, D. G. Truhlar, A. Fernández-Ramos (2020). “Pilgrim: A thermal rate constant calculator and a chemical kinetics simulator”. Comput. Phys. Commun., 256, 107457.
Pilgrim version 2021.5
MIT/X11 LICENSE
Copyright (c) 2021, David Ferro Costas (david.ferro@usc.es) and Antonio Fernandez Ramos (qf.ramos@usc.es)
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Contents of the folders distributed in this version:
Pilgrim is a program written in Python 3. Consequently, it does not need any kind of compilation, as it would be the case with C or Fortran programs. The user should install Python 3 in order to use Pilgrim, as well as the following Python libraries:
WARNING: DO NOT use Python 2 to execute Pilgrim.
Before using Pilgrim, the user has to define the path to the executable(s) of the software for the electronic structure calculation (ESSO). At the moment Pilgrim supports Gaussian and Orca as ESSO.
In order to interact with the ESSO, Pilgrim needs to know the location of some executable files. Such information is obtained from the following environment variables, which have to be defined and exported by the user in their .bashrc file:
For Gaussian users, the environment variables are:
Example of paths are:
export Gauexe="/home/programs/G09_64D/g09/g09" export GauFchk="/home/programs/G09_64D/g09/formchk" Similarly, for Orca users, this file has to contain the environment variable:
Example:
export OrcaExe="/home/programs/orca_4_0_1_2/orca" where, again, the path to the Orca executable is between quotation marks.
You can run Pilgrim by invoking the Python interpreter manually as follows:
python3 pilgrim.py
If you prefer to avoid invoking the Python interpreter, you have to follow these two simple steps:
Add as the first line in the pilgrim.py file the following:
#!PATH_FOR_PYTHON python
where PATH_FOR_PYTHON indicates the location of the Python interpreter. Example:
#!/usr/bin/python3
In this example Python is located in /usr/bin/.
Make the main program pilgrim.py executable:
chmod u+x pilgrim.py
This allows you to run Pilgrim just using:
pilgrim.py
Before running Pilgrim, we recommend to read the help menu. It can be displayed either by typing
pilgrim.py --help
or
pilgrim.py -h
Directory tests/ contains two subdirectories:
esfils/:
Includes the electronic structure files (ESFILs) with the
stationary points needed to run each of the working examples (WEs)
using Pilgrim. See the manual for details.
outputs/:
Includes the results of running the WEs. They can also be used
for comparison.
__examples_CPC/__:
Includes the examples described in Comput. Phys. Commun.