Quick 1D DVR

An interface of yDVR for non-programmer

Yu Zhai yuzhai@mail.huiligroup.org

Jilin University, Changchun, China

Introduction

You do not have to be a programmer to become an excellent scientist.

The Quick 1D DVR code is an interface of part of the functionality of yDVR for non-programmer.

Idea behind the code is to do a sinc-DVR calculation, with automatic converge check, etc.

In current version (v 0.4.0), I will focus on the energy only, since sinc-DVR eigenvectors are too large to use directly, in most cases.

Installation guide

As is said in the Introduction part, it is for the non-programmer, thus it is shipped with all its dependencies, including a copy of Eigen 3.3.7 and (one-dimension part of) yDVR 2.2.0.

To build it manually, simply type make quick1ddvr and press enter. As I tested, from g++-7 on and clang++-6.0 on (Ubuntu), should work. A new Ubuntu should shipped with gcc-9 by default. If a C++ compiler is not available, type

sudo apt install g++-7  # GCC 7 should be available on even an slightly old OS

On other distributions, similar installation can be done with their own package managements.

On Windows, TDM-GCC is used to build.

On Android, the program can be build on Termux.

On MacOS, tests are not done, because I do not have a Mac. However, in this project, I did not use any OS-specific code so it should be fine. If any problem occur, raise an issue on Github.

Also I provide an binary (for Linux) so the user can use it directly.

Maybe also an exe on Windows, let us see.

Usage

Usage: /path/to/quick1ddvr <filename>.inp

The input file should be a plain text file with format shown in sample/sample_hcl.inp. # is the starting of comments.

In the directory sample, input for HCl is given with all the output files. The users may want these files as a reference.

Keywords

The following keywords can be used.

Varaibles

• mass <mass>, reduced mass in amu, required.
• nlevels <n_levels>, number of excited state wanted, optional, default 5.
• threshold, converge energy threshold, optional, default 0.1 cm-1.
• fixboundary <a> <b> <ngrids>, perform a plain sinc-DVR computation with boundary and number of grinds fixed.

Units

By using this keywrods, you set the unit used in input file, as well as the std output. Extra output (eigenvectors, plots), however, will not be affected.

• Angstrom, length unit, default.
• Bohr, length unit.
• Hartree, energy unit.
• cm-1, energy unit, default.
• Kelvin, energy unit.
• eV, energy unit.

Potential energy curve

  pec
  <r1>    <V(r1)>
  <r2>    <V(r2)>
  <r3>    <V(r3)>
  ...
  <ri>    <V(ri)>
  ...
  <rn>    <V(rn)>
  endpec

Interesting features

• Quite a lot of suggestions will be given for the beginners during the execution. DVR method is (typically) not a dark-box, but I tried to make it one.

• The output *.plot.txt file aims to give a good input file for plotting. Use some software like Veusz, it is easy to draw some textbook-like figure, with the wave functions fluctuating around its energy level, localized in the potential well, like this

  

Troubleshooting

• If you use the binary, chances are that your get a Kernel too old error. A typically workaround is to compile it yourself. make should work.
• Please understand that it is your tech guy’s responsibility to update the operating system.

Information for developers

• I try to make the program easy to use for both end-user and developers. If you want to contribute to this program, go ahead.

• I use some terminal tools to develop this little project, including

  • Vim
  • GCC
  • Clang
  • GNU make
  • Valgrind

  I do not use an IDE. The reason is that I want the non-developers feel it easy to build, instead of having a copy of CMake, which have been used in yDVR, or some IDEs installed as prerequest.

• xtb from Prof. Grimme group is used to generate the test PEC. It can be found on Github. Although it is easy to used and I like it, I personally do not have any preference on choosing which quantum chemistry software to generate the PEC. You are welcomed to use any one, and leave a python script in the sample directory as a record.

• The robustness of the code is of number-one priority. Therefore, technically, memory-leaking and uninitialized variables are not acceptable. I use Valgrind to check. However, you have notice that the released binary version does not pass the check. That is because it is a statically linked version, and some "don't care" uninitialized variables are in like glibc, see discussion here. My work flow would be build a dynamically linked version (without the -static flag in the root Makefile, do the Valgrind check, and recompile it to a statically linked version.

Change log

• v 0.4.0 Update to yDVR 2.2.
• v 0.3.0 Largely optimize I/O.
• v 0.2.0 Add boundary check mechanism.
• v 0.1.0 Initial version.