No description, website, or topics provided.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
Eigen3
doc
include
src
tests
.DS_Store
Makefile
README.md
configure

README.md


LICHEM: Layered Interacting CHEmical Models

By: The Cisneros Research Group

Symbiotic Computational Chemistry

***

LICHEM: A QM/MM interface for polarizable force fields

GPL license

Automated tests

Introduction

This package is an open-source (GPLv3) interface between QM and MM software so that QM/MM calculations can be performed with polarizable and frozen electron density force fields. Functionality is also present for standard point-charge based force fields, pure MM, and pure QM calculations.

Available calculations: single-point energies, geometry optimizations, classical Monte Carlo, path-integral Monte Carlo, and reaction pathways.

Available QM wrappers: Gaussian, NWChem, PSI4

Available MM wrappers: TINKER

MM wrappers in development: LAMMPS

Citing LICHEM

If you use LICHEM in your research, please cite the following paper:

Kratz, E.G.; Walker, A.R.; Lagardere, L; Lipparini, F; Piquemal, J.-P.; and
Cisneros, G.A.; "LICHEM: A QM/MM Program for Simulations with Multipolar and
Polarizable Force Fields", J. Comput. Chem., 37, 11, 1019, (2016)

Installation

Currently, the binary and user's manual are not included in the repository. However, the Makefile can be used to generate both files. Since LICHEM is designed to be simple, only a small number of packages are required to compile the code. An approximate list of packages is given below.

 LICHEM binary: OpenMP, (MPI if hybrid-parallel QSM is desired)
 LICHEM test suite: Python
 LICHEM manual: LaTeX, BibTeX, TeXLive

A copy of the Eigen3 library is included with the LICHEM source code. However, other versions of Eigen3 can be used to build LICHEM by modifying the Makefile.

To install LICHEM, clone the git repository:

user:$ mkdir LICHEM
user:$ git clone https://github.com/CisnerosResearch/LICHEM.git ./LICHEM/

On Ubuntu boxes, the Makefile should function without modifications. However, it may be necessary to install additional LaTeX packages. On OSX machines, the SEDI, TEX, BIB, and CXXFLAGS variables will need to be modified. A configure file is provided to set up either serial or parallel build.

The Makefile can produce both the documentation and the binary.

user:$ ./configure
user:$ make install

For development, debugging, or testing an alternate binary can be compiled.

user:$ make Dev

Additional make rules can be found in the Makefile.

QM and MM packages

LICHEM uses QM and MM packages that are pre-installed and located in the user's path. The LICHEM wrappers are kept up-to-date with the development of the QM and MM packages. It is best to use packages from conda, git, or other package management systems.

Updates

LICHEM is still in the early stages of development. Please report all bugs so that the code can be updated quickly. Bugs should be reported through the GitHub issues interface. A list of known issues and the development timeline are available in the doc directory or on the GitHub page.

Development versions of LICHEM are kept in a private repository. Large changes to the code or the addition of new features (diffuse charges, reaction path ways, etc) are tested and published before they are merged into the public repository. To ensure that LICHEM compiles properly, dummy function calls are added for incomplete or untested features.

Relatively minor updates (documentation, output printing, bug fixes, comments, etc) are released ASAP. Updates from the private development branch are generally merged into the public repository as a single commit.

Further development details can be found in the doc directory, or the GitHub issues section.

Jokes

Jokes and Easter eggs can be included by changing

 const bool JOKES = 0; //Print humorous comments

in LICHEM_options.h to

 const bool JOKES = 1; //Print humorous comments

before compiling the code.

Testing

Test calculations can be performed with the runtests script in the tests directory.

Tests can be performed for pairs of QM and MM wrappers.

user:$ ./runtests Ncpus QMPackage MMPackage

Additionally, tests can be run for all wrappers at once.

user:$ ./runtests Ncpus All

A dry run can be performed to check packages without performing the calculations.

user:$ ./runtests Ncpus QMPackage MMPackage Dry

If tests are consistently failing, please post details on the GitHub issues section.

Development

The development of LICHEM was supported by funding from the NIH (Grant No. R01GM108583) and Wayne State University. LICHEM is maintained by the Cisneros research group at University of North Texas.

Developers:

  • Cisneros group, University of North Texas