Chemical concepts from wave function analysis

A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators.

Shortcuts

• Installation
• How to use
• Documentation
• Cite the code
• Bug reports and feature requests

Installation

Building from source

Prerequisites for manual installation

The code is currently set to be compiled using make and the following Intel oneAPI toolkits (available free of charge here):

• Intel oneAPI Base Toolkit
• Intel oneAPI HPC Toolkit

Compilation with profiling

1. Download source code from Github repository, for instance

git clone https://github.com/mgimferrer/APOST3D.git

2. Load the installed Intel oneAPI toolkits.

source /opt/intel/oneapi/setvars.sh intel64

Important: The compiler is installed by default in /opt. Change the path above to the appropriate location otherwise. Alternatively, load the appropriate modules created during the installation.

3. Set variable APOST3D_PATH to the destination folder (e.g. /home/user/APOST3D)

export APOST3D_PATH="/home/user/APOST3D"

4. Compile the provided Libxc libraries by executing the compile_libxc.sh script

Important: In case of using Intel oneAPI toolkits older than the 2024 version, replace export CC=icx by export CC=icc in compile_libxc.sh

Important: To date it is not possible to couple APOST-3D with newer Libxc libraries than the provided due to internal changes on the Libxc modules. We will work on that as soon as possible!

5. Set variable OMP_NUM_THREADS in make_compile.sh to the maximum number of threads (recommended the maximum in the machine)

6. Execute the make_compile.sh script

Important: This will first compile the code and run a series of tests (for about ca. 10 min) for profiling. A second compilation is then carried out using the profiling information (.dyn files), generating an apost3d executable that will run in using up to the number of threads defined in step #5. The tests are executed again, providing information about the profiled execution times.

How to use

The APOST-3D program runs using the apost3d executable located in $APOST3D_PATH.

## Load the compiler (alternatively, load the appropriate modules) ##
source /opt/intel/oneapi/setvars.sh intel64
## Set number of threads, stacksize and limits ##
export OMP_NUM_THREADS=48
export KMP_STACKSIZE=100m
ulimit -s unlimited

## Execute the program ##
$APOST3D_PATH/apost3d name-input > name-output.apost

Important: A name-input.fchk and name-input.inp files must be in the folder. A detailed description of the input file format is provided in the Documentation.

Documentation

The APOST-3D documentation is here.

Citations

Cite the code

The following paper should be cited in publications utilizing APOST-3D:

• P. Salvador, E. Ramos-Cordoba, M. Montilla, L. Pujal and M. Gimferrer, J. Chem. Phys., 2024, 160, 172502 DOI: 10.1063/5.0206187

Cite implemented methods

For atomic and overlap populations, bond orders and valences:

• I. Mayer and P. Salvador, Chem. Phys. Lett., 2004, 383, 368-375 DOI: 10.1016/j.cplett.2003.11.048

For Hartree-Fock molecular energy decomposition:

• P. Salvador, M. Duran and I.Mayer, J. Chem. Phys., 2001, 115, 1153-1157 DOI: 10.1063/1.1381407
• P. Salvador and I. Mayer, J. Chem. Phys., 2004, 120, 5046-5052 DOI: 10.1063/1.1646354

For KS-DFT molecular energy decomposition:

• P. Salvador and I. Mayer, J. Chem. Phys., 2007, 126, 234113 DOI: 10.1063/1.2741258
• M. Gimferrer and P. Salvador, J. Chem. Phys., 2023, 158, 234105 DOI: 10.1063/5.0142778

For CAS/DMRG molecular energy decomposition:

For origin-independent decomposition of static polarizabilities:

• M. Montilla, J. M. Luis and P. Salvador, J. Chem. Theor. Comput., 2021, 17, 1098-1105 DOI: 10.1021/acs.jctc.0c00926

For effective atomic/fragment orbitals:

• I. Mayer, J. Phys. Chem., 1996, 100, 6249 DOI: 10.1021/jp952779i
• I. Mayer and P. Salvador, J. Chem. Phys., 2009, 130, 234106 DOI: 10.1063/1.3153482
• E. Ramos-Cordoba, P. Salvador and I. Mayer, J. Chem. Phys., 2013, 138, 214107 DOI: 10.1063/1.4807775

For local spin analysis:

• E. Ramos-Cordoba, E. Matito, I. Mayer and P. Salvador, J. Chem. Theor. Comput., 2012, 8, 1270-1279 DOI: 10.1021/ct300050c
• E. Ramos-Cordoba, E. Matito, P. Salvador and I. Mayer, Phys. Chem. Chem. Phys., 2012, 14, 15291-15298 DOI: 10.1039/C2CP42513K

For effective oxidation states analysis:

• E. Ramos-Cordoba, V. Postils and P. Salvador, J. Chem. Theor. Comput., 2015, 11, 1501-1508 DOI: 10.1021/ct501088v
• M. Gimferrer and P. Salvador, submitted, 2024 DOI: XX

For oxidation states from localized orbitals:

• M. Gimferrer, G. Comas-Vila and P. Salvador, Molecules, 2020, 25, 234 DOI: 10.3390/molecules25010234
• M. Gimferrer, A. Aldossary, P. Salvador and M. Head-Gordon, J. Chem. Theor. Comput., 2022, 18, 309-322 DOI: 10.1021/acs.jctc.1c01011

For decomposition of EDA quantities into one- and two-center IQA terms:

• M. Gimferrer, S. Danes, D. M. Andrada and P. Salvador, J. Chem. Theory Comput., 2023, 19, 3469-3485 DOI: 10.1021/acs.jctc.3c00143

Bug reports and feature requests

Please submit tickets on the issues page, and/or send an email to mgimferrer18@gmail.com and pedro.salvador@udg.edu