std2 program for computing excited states and response functions via simplified TD-DFT methods (sTDA, sTD-DFT, SF-sTD-DFT, XsTDA, XsTD-DFT, and SF-Xs-TD-DFT)

This project provides the std2 program.

The std2 program is the rebranded and updated version of the stda program. Originally, stda was implemented only for the simplified time-dependent density functional theory using the Tamm-Dancoff approximation (sTDA) method. With the implementation of more simplified quantum chemistry (sQC) methods in stda, the name was not fitting the application of the program anymore.

Installation

Two options exist: make or meson.

Using make (and the intel compiler)

For that option, you need:

• cmake,
• the latest intel oneAPI Fortran compiler, ifx (not ifort), with MKL.

Then, you need to download the library to compute one- and two-electron integrals : libcint:

# create a `libcint` directory, then download sources in it
mkdir libcint
cd libcint
wget https://github.com/pierre-24/libcint-meson/releases/download/v0.3.0/libcint_v6.1.2.tar.gz -O libcint.tar.gz
tar -xzf libcint.tar.gz

The next step depends on your target. The default (32 bits integers, LP64) use a bit less memory but limits the size of the system you can treat. If you target large system, use the 64 bit integers (ILP64) instead.

32 bit integers (default, LP64)

First, build libcint:

# use intel
export CC=icx

# In the libcint directory, create a build directory and build `libcint` in it (using cmake)
mkdir build
cd build
cmake ..
cmake --build .

Then, compile std2 itself:

# go back
cd ../..

# make std2
make

64 bit integers (ILP64) for larger calculations

First, build libcint with the option for 64 bits integers:

export CC=icx

# In the libcint directory, create a build directory and build `libcint` in it (using cmake)
mkdir build
cd build
cmake .. -DI8=true
cmake --build .

Then, compile std2 itself:

# go back
cd ../..

# make std2 (using ILP64)
make USEILP64=1

Troubleshootings:

In some cases, the path to libraries is a bit different and the Makefile should be adapted as

LIBS = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -liomp5

Run

You will find a executable named std2 in this folder. To make std2 accessible, do:

export STD2HOME=/path/to/std2/folder
export LD_LIBRARY_PATH=$STD2HOME/libcint/build:$LD_LIBRARY_PATH
export PATH=$PATH:$STD2HOME

in your .bashrc or submission scripts.

Using meson (and any compiler)

Note that for the moment, it is not possible to use Meson to compile the 64 bit version with ifx (see there)

If you are not found of make, you can use meson and ninja instead. Other advantages include: automatic libcint import, more flexibility on the linear algebra backend and gfortran instead of intel.

First of all, if you want to use other compilers than gfortran, use:

# for latest version of intel compilers
export FC=ifx CC=icx

# for older versions of intel compilers
export FC=ifort CC=icc

Then, pick one of the meson setup line below:

# netlib BLAS and LAPACK, 32 bits integers
meson setup _build -Dla_backend=netlib

# openblas and netlib LAPACK, 32 bits integers
meson setup _build -Dla_backend=openblas

# MKL, 32 bits integers
meson setup _build -Dla_backend=mkl

# MKL, 64 bits integers (ILP64)
meson setup _build -Dla_backend=mkl -Dinterface=64

You can also:

• generate a statically linked executable by adding -Dstatic=true (only with MKL), or
• disable OpenMP (not recommended) by adding -Dopenmp=false.

And finally, compile everything with

meson compile -C _build

Run

You will an executable named std2 in the _build directory. To make std2 accessible, export

export STD2HOME=/path/to/std2/folder
export PATH=$PATH:$STD2HOME/_build/

in your .bashrc or submission scripts.

Usage

For parallel usage set the threads for OMP and the MKL linear algebra backend by

export OMP_NUM_THREADS=<ncores>

For larger systems please adjust the stack size accordingly, otherwise stack overflows will occur. Use something along the lines of this:

ulimit -s unlimited
export OMP_STACKSIZE=4G

See the manual on the release page.

Citations

• S. Grimme, A simplified Tamm–Dancoff density functional approach for the electronic excitation spectra of very large molecules, J. Chem. Phys., 2013, 138, 244104. DOI: 10.1063/1.4811331

• C. Bannwarth, S. Grimme, A simplified time-dependent density functional theory approach for electronic ultraviolet and circular dichroism spectra of very large molecules, Comput. Theor. Chem., 2014, 1040 – 1041, 45 – 53. DOI: 10.1016/j.comptc.2014.02.023

• S. Grimme and C. Bannwarth, Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB) J. Chem. Phys., 2016, 145, 054103. DOI: 10.1063/1.4959605

• M. de Wergifosse, S. Grimme, Nonlinear-response properties in a simplified time-dependent density functional theory (sTD-DFT) framework: Evaluation of the first hyperpolarizability, J. Chem. Phys., 2018, 149 (2), 024108. DOI: 10.1063/1.5037665

• M. de Wergifosse, S. Grimme, Nonlinear-response properties in a simplified time-dependent density functional theory (sTD-DFT) framework: Evaluation of excited-state absorption spectra, J. Chem. Phys., 2019, 150, 094112. DOI: 10.1063/1.5080199

• M. de Wergifosse, C. Bannwarth, S. Grimme, A simplified spin-flip time-dependent density functional theory (SF-sTD-DFT) approach for the electronic excitation spectra of very large diradicals, J. Phys. Chem. A, 2019, 123 (27), 815–5825. DOI: 10.1021/acs.jpca.9b03176

• M. de Wergifosse, J. Seibert, B. Champagne, and S. Grimme, Are fully conjugated expanded indenofluorenes analogues and diindeno[n]thiophene derivatives diradicals? A simplified (spin-flip) time-dependent density functional theory [(SF-)sTD-DFT] study, J. Phys. Chem. A, 2019, 123 (45), 9828-9839. DOI: DOI: 10.1021/acs.jpca.9b08474

• M. de Wergifosse, J. Seibert, S. Grimme, Simplified time-dependent density functional theory (sTD-DFT) for molecular optical rotation, J. Chem. Phys., 2020, 153, 084116. DOI: 10.1063/5.0020543

• M. de Wergifosse, S. Grimme, A unified strategy for the chemically intuitive interpretation of molecular optical response properties, J. Chem. Theory Comput., 2020, 16 (12), 7709–7720. DOI: 10.1021/acs.jctc.0c00990

• M. de Wergifosse, S. Grimme, Perspective on simplified quantum chemistry methods for excited states and response properties, J. Phys. Chem. A, 2021, J. Phys. Chem. A, 2021, 125 (18) 3841–3851. DOI: 10.1021/acs.jpca.1c02362

• P. Beaujean, B. Champagne, S. Grimme, and M. de Wergifosse, All-atom quantum mechanical calculation of the second-harmonic generation of fluorescent proteins, J. Phys. Chem. Lett., 2021, 12 (39), 9684-9690. DOI: 10.1021/acs.jpclett.1c02911

• M. de Wergifosse, P. Beaujean, S. Grimme, Ultrafast evaluation of two-photon absorption with simplified time-dependent density functional theory, J. Phys. Chem. A, 2022, 126 (41) 7534–7547. DOI: 10.1021/acs.jpca.2c02395

• S. Löffelsender, P. Beaujean, M. de Wergifosse. Simplified quantum chemistry methods to evaluate non-linear optical properties of large systems, WIREs Comput Mol Sci. 2024, 14 (1) e1695. DOI: 10.1002/wcms.1695

• M. de Wergifosse, S. Grimme, The eXact integral simplified time-dependent density functional theory (XsTD-DFT), J. Chem. Phys., 2024, 160, 204110. DOI: 10.1063/5.0206380

• M. de Wergifosse, Computing excited states of very large systems with range-separated hybrid functionals and the eXact integral simplified time-dependent density functional theory (XsTD-DFT), J. Phys. Chem. Lett., 2024, 15, (51) 12628–12635. DOI: 10.1021/acs.jpclett.4c03193

License

std2 is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

std2 is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU Lesser General Public License for more details.

Bugs

A bug is a demonstratable problem caused by the code in this repository. Good bug reports are extremely valuable for us - thank you!

Before opening a bug report:

1. Check if the issue has already been reported.
2. Check if it still is an issue or has already been fixed? Try to reproduce it with the latest version from the main branch.
3. Isolate the problem and create a reduced test case.

A good bug report should not leave others needing to chase you up for more information. So please try to be as detailed as possible in your report, answer at least these questions:

1. Which version of std2 are you using? The current version is always a subject to change, so be more specific. If possible, also provide the commit.
2. What is your environment (your laptop, the cluster of the university)?
3. What steps will reproduce the issue? We have to reproduce the issue, so we need all the input files.
4. What would be the expected outcome?
5. What did you see instead?

All these details will help people to fix any potential bugs.