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LIO Project

LIO is a Quantum Mechanical software based on Density Functional Theory (DFT) and real time Time Dependent Density Functional Theory (TD-DFT).

The most computationally intensive calculations are ported to use graphical processors which support CUDA (e.g. Nvidia Maxwell, Fermi, Kepler and Tesla families).

REQUIREMENTS

  • LAPACK or INTEL MKL.
  • GNU or INTEL C++ and Fortran Compiler.
  • NVIDIA CUDA (for the GPU kernels).
  • GNU Make.
  • Libxc for LIO (optional).

COMPILATION

The program can be compiled using the make command. The following options can be used to modify compilation. For example, the following compiles the GPU kernels:

make cuda=1 cpu=0

When using Intel's ICC/MKL or NVIDIA's CUDA libraries, add them to LD_LIBRARY_PATH environment variable before compilation. Available options for compilation include:

  • cpu: compile CPU kernels (default = 0).

  • cuda: compile GPU kernels (when = 1) and CUBLAS subroutines (when = 2). Used by default (=1).

  • intel: use INTEL compilers (when = 1) and INTEL MKL (when = 2). Not used by default (= 0).

  • analytics: Enables diferent levels of debug information and profiling (default = 0, max = 3).

  • precision: When precision = 1, compile everything in double precision (default = 0, hybrid precision).

  • libxc: compile the application to use libxc library. Requires libxc for lio installed.

INSTALLATION

Compilation will produce two dynamic libraries, which should be added to LD_LIBRARY_PATH and PATH environment variables.

  1. g2g/libg2g.so
  2. lioamber/liblio-g2g.so

Then set LIOHOME environment variable, pointing to LIO location.

INSTALLATION WITH AMBER

  1. Compile LIO as indicated above.
  2. Be sure to check (or edit if needed) the /src/configure2 file in AMBER so that liolibs variable correctly points to LIO library folders.
  3. Configure and compile AMBER with the -lio option (see Amber installation instructions).
  4. Done!

INSTALLATION WITH GROMACS

NOTE: GROMACS is not yet officially supported on the other side, but we have our own up-to-date Gromacs repository with the files needed.

  1. Compile LIO as indicated above.
  2. Compile GROMACS as usual, but changing compilation flags (see Gromacs installation instructions):
cmake -DGMX_GPU=0 -DGMX_THREAD_MPI=0 -DGMX_QMMM_PROGRAM="lio" -DLIO_LINK_FLAGS="-L/usr/lib -L/usr/lib64 -L/PATHTOLIOLIBRARIES -lg2g -llio-g2g"
  1. Done!

INSTALLATION WITH LIBXC

Currently there are two different implementations of the Libxc library, the original version (here) who runs all the functionals in cpu and the modified version (here) who runs some functionals in gpu. This version of Lio has support for both libraries depending on wich one you'll choose to use at runtime. You can use this version of Lio with both, one of none of the Libxc libraries. We'll recommend to have both installed.

In order to compile lio with libxc, follow the steps detailed below:

  1. Download the libxc cpu library. We recomend you to use libxc version 4.0.4.
  2. Compile and Install the cpu library (follow Libxc install instructions).
  3. Download the libxc gpu library.
  4. Compile and Install the library (follow the Libxc-gpu install instructions). Both the gpu and cpu libraries had to be installed in the same folder.
  5. In order for lio to compile with libxc, you'll need to create and export two environment variables in LD_LIBRARY_PATH
LIBXC_LIBS=points to the path where the libxc libaries where installed in the file system.
LIBXC_INCLUDES=points to the path where the libxc include files where installed in the file system.
  1. Go to the Libxc (gpu) installation folder and copy the next files into the LIBXC_INCLUDES folder defined in the step 5.
src/xc.h
src/xc_funcs.h
src/xc_funcs_removed.h
xc_version.h
  1. Libxc has 3 compilation options for lio, those are
libxc=0 - No libxc (DEFAULT - for backwards compatibility with lio)
libxc=1 - Use libxc in CPU mode
libxc=2 - Use libxc in GPU mode
  1. If you want to compile lio with libxc in GPU mode, type the following command
make cuda=1 libxc=2
  1. To validate the instalation, go to the integration-test folder located in lio/test/ and run the command make, this will compile and execute the integration test. After the execution of the test phase, you should see in the console:
Running gpu test...
gpu integration-test01:  0
gpu integration-test02:  0
gpu integration-test03:  0
Running cpu test...
cpu integration-test:  0

The 0 after each test means that the test ran without errors.

  1. To run the simulations using the functionals from libxc you'll have to add the following variables in the *****.in files:
file: agua.in

...
use_libxc=t
ex_functional_id=XXX
ec_functional_id=XXX
...

where ex_functional_id is the id for the exchange functional from libxc and ec_funcional_id is the id for the correlation functional from libxc. You can see the list of available functionals for gpu and the list of available functionals for cpu. Bare in mind that only the GGA functional's family are supported in this version of libxc for lio.

TESTS

The test suite can be ran from the tests directory, each subfolder contains a "correr.sh" script which performs the test.

CONTRIBUTING

Before contributing, make sure you have set up the git hooks for the project, and do read the wiki and workflow of the project.

PUBLICATIONS

  1. Matías A. Nitsche, Manuel Ferreria, Esteban E. Mocskos and Mariano C. González Lebrero, GPU Accelerated Implementation of Density Functional Theory for Hybrid QM/MM Simulations. J. Chem. Theory Comput., 2014, 10 (3), pp 959–967.

  2. Uriel N. Morzan, Francisco F. Ramírez, M. Belén Oviedo, Cristián G. Sánchez, Damián A. Scherlis and Mariano C. González Lebrero, Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework. J. Chem. Phys. 140, 164105 (2014).

  3. U. N. Morzan, F. Ramirez, M. Gonzalez Lebrero, D. Scherlis. Electron Transport in Real Time From First Principles. J. Chem. Phys. 146, 044110 (2017).

  4. J. P. Marcolongo, A. Zeida, J. A. Semelak, N. O. Foglia, U. N. Morzan, D. A. Estrin, M. C. González Lebrero and D. A. Scherlis. Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code. Front. Chem. (2018)