diff --git a/src/citeme.cpp b/src/citeme.cpp
index 9791d46f2..129ccbda6 100644
--- a/src/citeme.cpp
+++ b/src/citeme.cpp
@@ -1,187 +1,100 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "citeme.h"
#include "version.h"
#include "universe.h"
#include "comm.h"
#include <stdio.h>
#include <set>
using namespace LAMMPS_NS;
-#if 0
-// the list of publications is below
-static const char * const publication[] = {
- /* PLIMPTON_1995 */
- "S.J. Plimpton,\n"
- " Fast Parallel Algorithms for Short-Range Molecular Dynamics,\n"
- " J. Comp. Phys., 117, 1-19 (1995)\n\n",
- /* PLIMPTON_1997 */
- "S.J. Plimpton, R. Pollock, M. Stevens,\n"
- " Particle-Mesh Ewald and r-RESPA for Parallel Molecular Dynamics Simulations,\n"
- " Proc. of the 8th SIAM Conference on Parallel Processing for Scientific Computing,\n"
- " Minneapolis, MN (March 1997).\n\n",
- /* AUHL_2003 */
- "R. Auhl, R. Everaers, G.S. Grest, K. Kremer, S.J. Plimpton,\n"
- " Equilibration of long chain polymer melts in computer simulations,\n"
- " J. Chem. Phys., 119, 12718-12728 (2003)\n\n",
- /* JANSSENS_2006 */
- "K.G.F. Janssens, D. Olmsted, E.A. Holm, S.M. Foiles, S.J. Plimpton, P.M. Derlet,\n"
- " Computing the Mobility of Grain Boundaries,\n"
- " Nature Materials, 5, 124-127 (2006).\n\n",
- /* INTVELD_2008 */
- "P.J. in 't Veld, S.J. Plimpton, G.S. Grest,\n"
- " Accurate and Efficient Methods for Modeling Colloidal Mixtures in an\n"
- " Explicit Solvent using Molecular Dynamics,\n"
- " Comp. Phys. Comm., 179, 320-329 (2008).\n\n",
- /* PARKS_2008 */
- "M.L. Parks, R.B. Lehoucq, S.J. Plimpton, S.A. Silling,\n"
- " Implementing peridynamics within a molecular dynamics code,\n"
- " Comp. Phys. Comm., 179, 777-783 (2008)\n\n",
- /* MUKHERJEE_2008 */
- "R.M. Mukherjee, P.S. Crozier, S.J. Plimpton, K.S. Anderson,\n"
- " Substructured molecular dynamics using multibody dynamics algorithms,\n"
- " Intl. J. of Non-Linear Mechanics, 43, 1045-1055 (2008)\n\n",
- /* BROWN_2009 */
- "W.M. Brown, M.K. Petersen, S.J. Plimpton, and G.S. Grest,\n"
- " Liquid crystal nanodroplets in solution,\n"
- " J. Chem. Phys., 130, 044901 (2009)\n\n",
- /* THOMPSON_2009 */
- "A.P. Thompson, S.J. Plimpton, W. Mattson,\n"
- " General formulation of pressure and stress tensor for arbitrary many-body\n"
- " interaction potentials under periodic boundary conditions,\n"
- " J. Chem. Phys., 131, 154107 (2009)\n\n",
- /* PETERSEN_2010 */
- "M.K. Petersen, J.B. Lechman, S.J. Plimpton, G.S. Grest, P.J. in't Veld, P.R. Schunk,\n"
- " Mesoscale Hydrodynamics via Stochastic Rotation Dynamics:\n"
- " Comparison with Lennard-Jones Fluid,\n"
- " J. Chem. Phys., 132, 174106 (2010)\n\n",
- /* BROWN_2011 */
- "W.M. Brown, P. Wang, S.J. Plimpton, A.N. Tharrington,\n"
- " Implementing Molecular Dynamics on Hybrid High Performance Computers\n"
- " - Short Range Forces,\n"
- " Comp. Phys. Comm., 182, 898-911, (2011)\n\n",
- /* BROWN_2012 */
- "W.M. Brown, A. Kohlmeyer, S.J. Plimpton, A.N. Tharrington,\n"
- " Implementing Molecular Dynamics on Hybrid High Performance Computers\n"
- " - Particle-Particle Particle-Mesh,\n"
- " Comp. Phys. Comm., 183, 449-459 (2012)\n\n",
- /* JARAMILLO_BOTERO_2011 */
- "A. Jaramillo-Botero, J. Su, A. Qi, W.A. Goddard III,\n"
- " Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics\n"
- " for Describing Material Properties and Phenomena in Extreme Environments,\n"
- " J. Comp. Chem., 32, 497-512 (2011)\n\n",
- /* KONG_2011 */
- "L.T. Kong,\n"
- " Phonon dispersion measured directly from molecular dynamics simulations,\n"
- " Comp Phys Comm, 182, 2201-2207 (2011)\n\n",
- /* AKTULGA_2012 */
- "H.M. Aktulga, J.C. Fogarty, S.A. Pandit, A.Y. Grama,\n"
- " Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques,\n"
- " Parallel Computing, 38, 245-259 (2012)\n\n",
- /* PLIMPTON_2012 */
- "S.J. Plimpton and A.P. Thompson,\n"
- " Computational Aspects of Many-body Potentials,\n"
- " MRS Bulletin, 37, 513-521 (2012)\n\n",
- /* SIRK_2013 */
- "T.W. Sirk, S. Moore, E.F. Brown,\n"
- " Characteristics of thermal conductivity in classical water models,\n"
- " J. Chem. Phys., 138, 064505 (2013)\n\n",
- /* FIORIN_2013 */
- "G. Fiorin, M.L. Klein and J. Henin,\n"
- " Using collective variables to drive molecular dynamics simulations,\n"
- " Mol. Phys. http://dx.doi.org/10.1080/00268976.2013.813594 (2013)\n\n",
- NULL
-};
-#endif
-
-
// to simplify the code below
typedef std::set<const char *> citeset;
static const char nagline[] = "\n"
"------------------------------------------------------------------------\n"
"This simulation made use of algorithms and methodologies described\n"
"in the references listed in the file 'log.cite'\n"
"------------------------------------------------------------------------\n";
static const char cite_header[] = "\n"
"------------------------------------------------------------------------\n"
"This simulation made use of algorithms and methodologies described\n"
"in the following references:\n\n";
static const char lammps_version[] =
"The LAMMPS Molecular Dynamics Simulator, Version " LAMMPS_VERSION "\n"
" http://lammps.sandia.gov\n\n";
/* ---------------------------------------------------------------------- */
CiteMe::CiteMe(LAMMPS *lmp) : Pointers(lmp) {
FILE *fp;
citeset *c = new citeset;
_pubs = (void *)c;
if ((universe->me == 0) && ((fp = fopen("log.cite","w")))) {
fputs(cite_header,fp);
fputs(lammps_version,fp);
fflush(fp);
} else {
fp = NULL;
}
_fp = (void *) fp;
}
/* ----------------------------------------------------------------------
Write out and register a citation so it will be written only once
------------------------------------------------------------------------- */
void CiteMe::add(const char *ref)
{
citeset *c = (citeset *) _pubs;
if (c->find(ref) == c->end()) {
FILE *fp = (FILE *)_fp;
fputs(ref,fp);
fflush(fp);
c->insert(ref);
}
}
/* ----------------------------------------------------------------------
Write out nag-line at the end of the regular output and clean up.
------------------------------------------------------------------------- */
CiteMe::~CiteMe()
{
if (comm->me == 0) {
if (screen)
fputs(nagline,screen);
if (logfile)
fputs(nagline,logfile);
}
FILE *fp = (FILE *)_fp;
if (fp) fclose(fp)
citeset *c = (citeset *) _pubs;
delete c;
}