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Polyrate 17-C on Allwinner D1

Introduction

Polyrate 17-C is a suite of computer programs for the calculation of chemical reaction rates of polyatomic species (including atoms and diatoms as special cases) by variational transition state theory (VTST); conventional transition state theory is also supported. Polyrate 17-C (called Polyrate for short) consists of the main program, called Polyrate, and a set of utility codes.

Polyrate - version 17-C is licensed under the Apache License, Version 2.0.

The manual of Polyrate - version 17-C is licensed under CC-BY-4.0.

Platform

  • SBC: Mango Pi MQ Pro with Allwinner D1 and 1 GB RAM
  • OS: Ubuntu 22.04.2 LTS riscv64
  • Compilers: gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu1~22.04.1)

Prerequests

  • csh
  • make
  • GNU Compilers, including gcc, g++, and gfortran

If not installed, install them via apt.

$ ubuntu@ubuntu:~$ sudo apt install csh make gcc g++ gfortran -y

Installation

First, download Polyrate 17-C from its release site: https://comp.chem.umn.edu/sds/polyrate/polyrate.cgi and upload the file polyrate17C_20190728_withSSQRRK_20190110.tar.gz to Mango Pi MQ Pro.

Since Polyrate will create 2 files at one's home directory named .poly_path and .poly_ver during the installation, it is recommanded to remove these files.

ubuntu@ubuntu:~$ rm .poly_path .poly_ver

Then decompress Polyrate package. Once finished, a directory named polyrate17 can be found.

ubuntu@ubuntu:~$ tar zxvf polyrate17C_20190728_withSSQRRK_20190110.tar.gz

Enter polyrate17, and run the script configure. When asked to choose between RP-VTST or VRC-VTST, type RP and return.

ubuntu@ubuntu:~/polyrate17$ ./configure

Welcome to POLYRATE!


                            Notice to users
 ************************************************************************
 Starting from version 2008, POLYRATE has two kinds of executables:

 1. RP-VTST for reactions with potential energy barriers (serial code)
 2. VRC-VTST for barrierless bimolecular association reactions (MPI code)

 RP-VTST and VRC-VTST need different executables and they should be
 compiled separately by running this script
 ************************************************************************

 Cleaning the src/ directory ...

... processor is riscv64
... OS is Linux

Is this running used to generate Makefile for RP-VTST or VRC-VTST?
 [ Choose 'RP' or 'VRC' ]: RP
....did not find Intel Fortran compiler - ifort
....found GNU Fortran compiler - gfortran :/usr/bin/gfortran
....found MPI compiler :/usr/bin/mpif77
....did not find Intel C compiler
....found GNU C compiler :/usr/bin/gcc
....found MPI C compiler :/usr/bin/mpicc

 Do the options chosen above look OK? [ yes ]:
... installing
.... creating Makefile

---- POLYRATE INSTALLATION COMPLETE ----

Have a nice day! :)

.... done with Makefile

Even Polyrate wishes us a nice day, the Makefile has to be modified manually cause the codes are too ancient for gfortran-11 to compile. Open the Makefile in directory src, the first line shall be

F77C    = /usr/bin/gfortran -O -fno-automatic

The only thing you should do is to add -std=legacy after /usr/bin/gfortran, and this line should looks like

F77C    = /usr/bin/gfortran -std=legacy -O -fno-automatic

Now the installation is done , and Have a nice day! :).

Tests

Polyrate offers some tests under polyrate17/testrun, in order to run all tests for RP-VTST version, simply type ./run_allPRVTST.jc. All scripts in Polyrate are written in csh. For the tests jobs shares mounds of codes that provides the molecular dynamics algorithms, the mainly differences between each systems are the potential energy surfaces and input files. Once a job runs under a fresh-installed Polyrate, which may be very slow on SBCs for compiling the shared codes, it will never be such painful to run other jobs.

Results

System Elapsed Time
1 h3 0:07.70
2 cwmc 0:51.16
3 ch4oh 0:02.99
4 ch4o 0:21.46
5 ch5 1:41.01
6 ch4cl 0:01.10
7 oh3 0:42.46
8 ho2 1:07.09
9 clhbr 0:31.21
10 cmc 0:19.73
11 nh3 0:02.93
12 hni 0:35.17
13 h2ni 0:15.29
14 ohcl 0:54.14
15 h3o2 0:01.87

Reference

(1) Isaacson, A. D.; Truhlar, D. G.; Rai, S. N.; Steckler, R.; Hancock, G. C.; Garrett, B. C.; Redmon, M. J. POLYRATE: A General Computer Program for Variational Transition State Theory and Semiclassical Tunneling Calculations of Chemical Reaction Rates. Comput. Phys. Commun. 1987, 47 (1), 91–102. https://doi.org/10.1016/0010-4655(87)90069-5.