=====================================
GENESIS 2.1.0
=====================================

GENESIS website
===============
https://www.r-ccs.riken.jp/labs/cbrt/


Installation Guide
==================

### General

To install cgdyn, please follow these steps:

  1. Type `autoreconf`.
  2. Type `./configure --enable-mixed`. You can specify MPI Fortran and C compilers by defining `FC` and `CC`.
     Example: `./configure --enable-mixed FC=mpif90 CC=mpicc`.
  3. Navigate to the `src/cgdyn` directory.
  4. Type `make`.
  5. Now you can execute MD simulations using the `cgdyn` binary generated in the `src/cgdyn` directory.


### MacOS users

We have not extensively tested our code with the default LLVM compilers shipped with MacOS.
Please use tools like Homebrew to install GNU compilers and perform the following steps before proceeding with the installation steps described in the General section:

  - `export OMPI_CC=gcc-13`
  - `export OMPI_CXX=g++-13`

  More information of installation can be found from https://www.r-ccs.riken.jp/labs/cbrt/installation/
  
  Typically, the installation process takes less than 10 minutes. For faster installation, use `make -j` (for example, `make -j4`).


Documentation
=============

- Demo and tutorials: https://www.r-ccs.riken.jp/labs/cbrt/tutorials2022/
- Instructions for use: https://github.com/RikenSugitaLab/cgdyntest


Contributors
============

Project Leader: Yuji Sugita (RIKEN)

  Current main developers:
  Jaewoon Jung (RIKEN), 
  Shingo Ito (RIKEN), 
  Chigusa Kobayashi (RIKEN),
  Takaharu Mori (RIKEN), 
  Hiraku Oshima (RIKEN),
  Cheng Tan (RIKEN),
  Diego Ugarte (RIKEN),
  Kiyoshi Yagi (RIKEN). 

  Other developers/contributors for older versions:
  Motoshi Kamiya (RIKEN), 
  Kento Kasahara (RIKEN/Osaka Univ.), 
  Yasuhiro Matsunaga (RIKEN/Saitama University)
  Daisuke Matsuoka (RIKEN/RIST), 
  Osamu Miyashita (RIKEN), 
  Suyong Re (RIKEN/NIBIOHN),
  Ai Shinobu (RIKEN),
  Yosuke Sumiya (RIKEN),
  Florence Tama (RIKEN/Nagoya University),
  Shoji Takada (Kyoto Univ.),
  Isseki Yu (RIKEN/Maebashi Institute of Technology).

  Tadashi Ando (RIKEN),
  Michael Feig (Michigan State University), 
  Raimondas Galvelis (RIKEN),
  Ryuhei Harada (RIKEN), 
  Takashi Imai (RIKEN), 
  Yasuaki Komuro (RIKEN), 
  Yasuhito Karino (RIKEN),
  Naoyuki Miyashita (RIKEN), 
  Wataru Nishima (RIKEN),
  Donatas Surblys (RIKEN),
  Koichi Tamura (RIKEN), 
  Kenta Yamada (RIKEN), 
  Takao Yoda (Nagahama Institute of Bio-Science and Technology),

  Acknowledgments: 
  Norio Takase (Isogo Soft), Yasumasa Joti (RIKEN SPring8),
  Akira Naruse (NVIDIA), Yukihiko Hirano (NVIDIA Japan),
  Hikaru Inoue (Fujitsu Ltd.), Tomoyuki Noda (Fujitsu Ltd.),
  Kiyotaka Sakamoto (Fujitsu Ltd.), Yoshinobu Akinaga (VINAS),
  Yoshitake Sakae (RIST), Nobuhiko Kato (ASTOM R&D),
  Toru Shiozaki (QSimulate), Klaas Gunst (QSimualte),
  Hideyo Yoshida (JSOL Corporation), Kenta Chaki (JSOL Corporation),
  Kazuhiro Hashiba (VINAS)

  Copyright (C) 2014-2022 RIKEN. All Rights Reserved

What is GENESIS?
================
GENESIS (GENeralized-Ensemble SImulation System) is a suite of 
computer programs for carrying out molecular dynamics simulations 
of biomolecular systems. 

GENESIS is free software, distributed under the GNU Lesser General Public
License version 3 or later. You can freely redistribute it and/or
modify it as a derived work under the terms of LGPL v3 or later. 
If possible, however, it would be greatly appreciated if you send us
feedbacks. Your cooperation helps us to keep developing and managing
this official GENESIS, providing all other GENESIS users qualified
codes.

Citation Information
====================
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita,
"GENESIS: A hybrid parallel and multi-scale molecular dynamics simulator
with enhanced sampling algorithms for biomolecular and cellular simulations",
WIREs Computational Molecular Science, 5, 310-323 (2015).
DOI: 10.1002/wcms.1220

C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, 
M. Kamiya, and Y. Sugita, 
"GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced 
sampling algorithms on multiple computational platforms",
J. Compute. Chem. 38, 2193-2206 (2017).
DOI: 10.1002/jcc.24874

Copyright Notices
=================
  Copyright (C) 2014-2022 RIKEN.

  GENESIS is free software; you can redistribute it and/or
  modify it provided that the following conditions are met:

  (1) All publications and commercial products using this software should cite 
      the above references, Jung et al (2015) and Kobayashi et al (2017).

  (2) In addition, proper citations should be given for each specific 
      methods used. Visit the website,
        https://www.r-ccs.riken.jp/labs/cbrt/citations/
      to see how to cite the original papers.

  (3) We ask the users to make their best effort to cite the papers in 
      the **main text**. Although it is permitted to cite some of the papers in
      the supporting information / supplementary materials due to the limitation of
      article length, the name of the software, GENESIS, and at least one of the
      papers should appear in the main text.

  GENESIS is released under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 3 of the License, or (at your option) any later version.
  
  GENESIS 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 Lesser General Public
  License along with GENESIS -- see the file COPYING and COPYING.LESSER.
  If not, see https://www.gnu.org/licenses/.
 
It should be mentioned this package contains the following softwares
for convenience. Please note that these are not covered by the license
under which a copy of GENESIS is licensed to you, while neither
composition nor distribution of any derivative work of GENESIS with
these software violates the terms of each license, provided that it meets
every condition of the respective licenses.

SIMD-oriented Fast Mersenne Twister (SFMT)
-------------------------------------------
SFMT is a new variant of Mersenne Twister (MT) introduced by Mutsuo
Saito and Makoto Matsumoto in 2006. The algorithm was reported at
MCQMC 2006. The routine is distributed under the New BSD License.

  Copyright (c) 2006,2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima University.
  Copyright (c) 2012 Mutsuo Saito, Makoto Matsumoto,
  Hiroshima University and The University of Tokyo.
  All rights reserved.

  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions
  are met:

  * Redistributions of source code must retain the above copyright
  notice, this list of conditions and the following disclaimer.
  * Redistributions in binary form must reproduce the above
  copyright notice, this list of conditions and the following
  disclaimer in the documentation and/or other materials provided
  with the distribution.
  * Neither the names of Hiroshima University, The University of
  Tokyo nor the names of its contributors may be used to endorse
  or promote products derived from this software without specific
  prior written permission.

  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
  LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
  A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
  OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
   (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
   OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

FFTE: A Fast Fourier Transform Package
--------------------------------------
FFTE (http://www.ffte.jp/) is written by Daisuke Takahashi (Tsukuba
University).

  Copyright (C) 2000-2004, 2008-2011 Daisuke Takahashi (Tsukuba
  University).

  You may use, copy, modify this code for any purpose (include
  commercial use) and without fee. You may distribute this ORIGINAL
  package.

Complementary error function: erfc04
------------------------------------
A Complementary error function routine (erfc04) is written by SunSoft,
a Sun Microsystems, Inc. business.

  Copyright (C) 1993 Sun Microsystems, Inc.

  Developed at SunSoft, a Sun Microsystems, Inc. business.
  Permission to use, copy, modify, and distribute this
  software is freely granted, provided that this notice
  is preserved (see at_energy_pme.fpp, and sp_energy_pme.fpp).

L-BFGS-B (version 3.0)
----------------------

L-BFGS-B (http://users.iems.northwestern.edu/~nocedal/lbfgsb.html)
is written by C. Zhu, R. Byrd, J. Nocedal and J. L. Morales. 

   This software is freely available, but we expect that all publications 
   describing work using this software, or all commercial products using 
   it, quote at least one of the references given below. This software is 
   released under the "New BSD License" (aka "Modified BSD License" or 
   "3-clause license"). 

   R. H. Byrd, P. Lu and J. Nocedal.  
   A Limited Memory Algorithm for Bound Constrained Optimization, 
   (1995), SIAM Journal on Scientific and Statistical Computing, 
   16, 5, pp. 1190-1208.

   C. Zhu, R. H. Byrd and J. Nocedal. 
   L-BFGS-B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale 
   bound constrained optimization 
   (1997), ACM Transactions on Mathematical Software, 
   Vol 23, Num. 4, pp. 550-560.

   J.L. Morales and J. Nocedal. 
   L-BFGS-B: Remark on Algorithm 778: L-BFGS-B, FORTRAN routines for 
   large scale bound constrained optimization 
   (2011), ACM Transactions on Mathematical Software, 
   Vol 38, Num. 1, Article No. 7.

JSON-Fortran (version 8.2.5)
----------------------------

JSON-Fortran (https://github.com/jacobwilliams/json-fortran)
developed by J. Williams, is a user-friendly, thread-safe, and object-oriented 
API for reading and writing JSON files, written in modern Fortran

   The JSON-Fortran source code and related files and documentation are distributed
   under a permissive free software license (BSD-style). See the LICENSE file
   (src/lib/json-fortran/LICENSE) for more details.