Critic2 is a program for the topological anaylisis of real-space scalar fields in periodic systems. The functionality includes Bader's atoms in molecules theory (critical point search, basin integration via different methods, basin plotting,...), analysis of other chemically-interesting fields (e.g. elf, laplacian of the density,...), non-covalent interaction plots (NCIplots), and much more.
Critic2 is designed to provide an abstraction layer on top of the underlying electronic structure calculation. Different methods (FPLAPW, pseudopotentials, local orbitals,...) represent the electron density and other fields in diverse ways. Critic2 interfaces to many of these and applies common techinques and algorithms to them. At the moment of writing this, critic2 can interface to WIEN2k, elk, PI, Quantum ESPRESSO, abinit, VASP, and any program capable of writing the scalar field of interest to a grid.
The electron density is the usual field critic2 works with, but any other (ELF, molecular electrostatic potential,...) can be analysed using the same techniques. Hence, it is possible to compute, for instance, the charges inside the basins of ELF, or the gradient paths of the molecular electrostatic potential. New scalar fields can be computed using critic2's powerful arithmetic expressions.
- README: this file.
- AUTHORS: the authors of the package.
- LICENSE: a copy of the licence. Critic2 is distributed under the GNU/GPL license v3.
- NEWS: a summary of changes from the last stable version.
- INSTALL: installation instructions.
- THANKS: acknowledgements. Please read this for details on the license of code that critic2 uses.
- src/: source code.
- doc/: documentation (user's guide) and syntax reference (syntax.txt).
- tools/: some tools to work with the files produced by critic2.
- dat/: atomic density and cif database data.
If you got the code from the git repository and not from a package, you will need to run:
autoreconf -i
Prepare for compilation doing:
./configure
Use configure --help for information about the
compilation options. The --prefix option sets the installation
path; more details about configure can be found in the INSTALL
file. Once critic2 is configured, compile using:
make
This should create the critic2 executable inside the src/ subdirectory. The binary can be used directly or the entire critic2 distribution can be installed to the 'prefix' path by doing:
make install
Critic2 is parallelized for shared-memory architectures (unless compiled with --disable-openmp). You modify the number of parallel threads by setting the OMP_NUM_THREADS environment variable. The following are parallelized in critic2:
- CP search (over starting seeds)
- Bisection (over integration rays)
- Generation of 3D grids in CUBE, WRITE,... (over planes)
- Qtree (over tetrahedra)
Note that the compilation flags for compilers different from ifort and gfortran regarding parallelization may not be correct.
The environment variable CRITIC_HOME is necessary if critic2 was not installed with 'make install'. It must point to the root directory of the distribution:
export CRITIC_HOME=/home/alberto/programs/critic2dir
This variable is necessary for critic2 to find the atomic densities, the cif dictionary and the library data. These should be located in ${CRITIC_HOME}/dat/.
Some notes:
-
Older versions of the intel fortran compiler have a bug in how openmp deals with allocatable arrays which affects the qtree integrator and maybe other parts of the code. These problems have been solved in version 13.1.
-
critic2 as it is distributed can be compiled only with the more recent versions of gfortran (somewhere along 4.8.x, and all versions starting at 4.9). If a recent compiler is not available, a possibility is to compile the program elsewhere with the static linking option:
LDFLAGS=-static ./configure ...
Critic2 can be compiled with libxc support. Libxc is used in critic2 to calculate exchange and correlation energy densities via the xc() function in arithmetic expressions. To do this, the --with-libxc options must be passed to configure:
./configure --with-libxc-prefix=/opt/libxc --with-libxc-include=/opt/libxc/include
Here the /opt/libxc directory is the target for the libxc installation (use --prefix=/opt/libxc when you configure libxc). Make sure that you use the same compiler for libxc and for critic2; otherwise the library will not be linked. You can choose the compiler by changing the FC and F77 flags before configure:
FC=gfortran F77=gfortran ./configure ...
See 'Use of LIBXC in arithmetic expressions' in the user's guide for instructions on how to use libxc in critic2.
The user's guide is in the doc/ directory in plain text (user-guide.txt). A copy of the manual in PDF format (user-guide.pdf) can be generated by running the compile.sh script. This requires a working LaTeX installation, the rst2latex program (included in the docutils package), and awk. A concise summary of the syntax can be found in the syntax.txt file. Several examples are provided in the examples/ subdirectory.
Critic2 reads a single input file (the cri file). A simple input is:
crytal cubicBN.cube
load cubicBN.cube
zpsp B 3 N 5
yt
which reads the crystal structure from a cube file, then the electron density from the same cube file, and then calculates the atomic charges and volumes. Run critic2 as:
critic2 cubicBN.cri cubicBN.cro
A detailed description of the keywords accepted by critic2 is given in the user's guide and a short reference in the syntax.txt file.
The basic references for critic2 are:
- A. Otero-de-la-Roza, E. R. Johnson and V. Luaña, Comput. Phys. Commun. 185, 1007-1018 (2014) (http://dx.doi.org/10.1016/j.cpc.2013.10.026)
- A. Otero-de-la-Roza, M. A. Blanco, A. Martín Pendás and V. Luaña, Comput. Phys. Commun. 180, 157–166 (2009) (http://dx.doi.org/10.1016/j.cpc.2008.07.018)
See the outputs and the manual for references pertaining particular keywords.
Copyright (c) 2013-2015 Alberto Otero de la Roza, Ángel Martín Pendás and Víctor Luaña.
critic2 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
critic2 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 General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.