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             README file for Cube3D
                 February, 2024

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What is Cube3D?

Cube3d is a code part of the GPUAM project designed to search for critical points of scalar fields that are used in computational/quantum chemistry such as electron density. This search is carried out completely numerically and takes as input a file in the Gaussian "cube" format.

This code has been developed at the UAM-I (Metropolitan Autonomous University

• Iztapalapa) in the area of Theoretical Physical Chemistry and updated during my postdoctoral stays at McMaster University and Argonne National Lab.

Perform a completely numerical search using 3-dimensional Lagrange interpolators.

How to install?

To install it, download the latest version from the GitHub repository. Go to the src subdirectory, inside you will find a makefile file, which has all the information necessary to compile it. This is a code that is parallelized at the OMP level, so it is beneficial to have the OMP library.

Inside src type make

$ make
gcc -c -Wunused  -Wno-unused-result -O2 main.c
gcc -c -Wunused  -Wno-unused-result -O2 -DD file.c
gcc -c -Wunused  -Wno-unused-result -O2 array.c
gcc -c -Wunused  -Wno-unused-result -O2 graph.c
gcc -c -Wunused  -Wno-unused-result -O2 fields.c -fopenmp
gcc -c -Wunused  -Wno-unused-result -O2 transU.c
gcc -c -Wunused  -Wno-unused-result -O2 tableP.c
gcc -c -Wunused  -Wno-unused-result -O2 timing.c
gcc -c -Wunused  -Wno-unused-result -O2 jacobi.c
gcc -c -Wunused  -Wno-unused-result -O2 -DGRAPH  kernels.c
gcc -c -Wunused  -Wno-unused-result -O2 lagForm.c
gcc -c -Wunused  -Wno-unused-result -O2 lebedev.c
gcc -c -Wunused  -Wno-unused-result -O2 lectura.c
gcc -c -Wunused  -Wno-unused-result -O2 findCrit.c -fopenmp
gcc -c -Wunused  -Wno-unused-result -O2 geomData.c
gcc -c -Wunused  -Wno-unused-result -O2 rotation.c
gcc -c -Wunused  -Wno-unused-result -O2 cubeIndex.c
gcc -c -Wunused  -Wno-unused-result -O2 lagrange2.c
gcc -c -Wunused  -Wno-unused-result -O2 replicate.c
gcc -c -Wunused  -Wno-unused-result -O2 mathTools.c
gcc -c -Wunused  -Wno-unused-result -O2 numBondPath.c -fopenmp
gcc -c -Wunused  -Wno-unused-result -O2 runCommands.c -fopenmp
gcc -c -Wunused  -Wno-unused-result -O2 utils.c
gcc -o cube3D.x main.o file.o array.o graph.o fields.o transU.o tableP.o timing.o jacobi.o kernels.o lagForm.o lebedev.o lectura.o findCrit.o geomData.o rotation.o cubeIndex.o lagrange2.o replicate.o mathTools.o refinement.o numBondPath.o runCommands.o utils.o -lm  -fopenmp

and finally, install by the next command:

$ make install

The binary is located in /home/USER/bin/cube3d.x.

Make sure to export this subdirectory in your PATH so you can invoke it from any location.

$ export PATH= $PATH:/home/USER/bin/cube3d.x

First steps

Once the binary is installed and the location of the binary is exported in the path, you can go to proof subdir. There is an example cube file, called ureaII.cube which corresponds to a urea crystal. To generate an input file type the following.

cube3d.x -f ureaII.cube -i input.in

This will create a cube3d input file, the input file contains the information to run cube3d, the name of the cube file, the tasks it can evaluate, and various extra options. Take a look at that file.