git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10492 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/pair_gayberne.cpp

@@ -28,15 +28,29 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "integrate.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 
+static const char cite_pair_gayberne[] =
+  "pair gayberne command:\n\n"
+  "@Article{Brown09,\n"
+  " author =  {W. M. Brown, M. K. Petersen, S. J. Plimpton, and G. S. Grest},\n"
+  " title =   {Liquid crystal nanodroplets in solution},\n"
+  " journal = {J.~Chem.~Phys.},\n"
+  " year =    2009,\n"
+  " volume =  130,\n"
+  " pages =   {044901}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 PairGayBerne::PairGayBerne(LAMMPS *lmp) : Pair(lmp)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_pair_gayberne);
+
   single_enable = 0;
 }
 

src/GPU/fix_gpu.cpp

@@ -19,7 +19,6 @@
 #include "pair.h"
 #include "respa.h"
 #include "input.h"
-#include "error.h"
 #include "timer.h"
 #include "modify.h"
 #include "update.h"
@@ -27,6 +26,8 @@
 #include "universe.h"
 #include "gpu_extra.h"
 #include "neighbor.h"
+#include "citeme.h"
+#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -42,11 +43,32 @@ extern void lmp_clear_device();
 extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
                              double **vatom, double *virial, double &ecoul);
 
+static const char cite_gpu_package[] =
+  "GPU package (short-range and long-range):\n\n"
+  "@Article{Brown11,\n"
+  " author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},\n"
+  " title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},\n"
+  " journal = {Comp.~Phys.~Comm.},\n"
+  " year =    2011,\n"
+  " volume =  182,\n"
+  " pages =   {898--911}\n"
+  "}\n\n"
+  "@Article{Brown12,\n"
+  " author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},\n"
+  " title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},\n"
+  " journal = {Comp.~Phys.~Comm.},\n"
+  " year =    2012,\n"
+  " volume =  183,\n"
+  " pages =   {449--459}\n"
+  "}\n\n"
+
 /* ---------------------------------------------------------------------- */
 
 FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_gpu_package);
+
   if (lmp->cuda)
     error->all(FLERR,"Cannot use fix GPU with USER-CUDA mode enabled");
 

src/MC/fix_bond_swap.cpp

@@ -29,6 +29,7 @@
 #include "modify.h"
 #include "compute.h"
 #include "random_mars.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -37,11 +38,24 @@
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
+static const char cite_fix_bond_swap[] =
+  "neighbor multi command:\n\n"
+  "@Article{Auhl03,\n"
+  " author = {R. Auhl, R. Everaers, G. S. Grest, K. Kremer, S. J. Plimpton},\n"
+  " title = {Equilibration of long chain polymer melts in computer simulations},\n"
+  " journal = {J.~Chem.~Phys.},\n"
+  " year =    2003,\n"
+  " volume =  119,\n"
+  " pages =   {12718--12728}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 FixBondSwap::FixBondSwap(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_bond_swap);
+
   if (narg != 6) error->all(FLERR,"Illegal fix bond/swap command");
 
   vector_flag = 1;

src/MISC/fix_orient_fcc.cpp

@@ -28,10 +28,11 @@
 #include "neigh_request.h"
 #include "comm.h"
 #include "output.h"
+#include "force.h"
 #include "math_const.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -39,11 +40,24 @@ using namespace MathConst;
 
 #define BIG 1000000000
 
+static const char cite_fix_orient_fcc[] =
+  "fix orient/fcc command:\n\n"
+  "@Article{Janssens06,\n"
+  " author = {K. G. F. Janssens, D. Olmsted, E.A. Holm, S. M. Foiles, S. J. Plimpton, and P. M. Derlet},\n"
+  " title = {Computing the Mobility of Grain Boundaries},\n"
+  " journal = {Nature Materials},\n"
+  " year =    2006,\n"
+  " volume =  5,\n"
+  " pages =   {124--127}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_orient_fcc);
+
   MPI_Comm_rank(world,&me);
 
   if (narg != 11) error->all(FLERR,"Illegal fix orient/fcc command");

src/PERI/atom_vec_peri.cpp

@@ -23,6 +23,7 @@
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -30,10 +31,23 @@ using namespace LAMMPS_NS;
 
 #define DELTA 10000
 
+static const char cite_peri_package[] =
+  "PERI package for Peridynamics:\n\n"
+  "@Article{Parks08,\n"
+  " author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
+  " title = {Implementing peridynamics within a molecular dynamics code},\n"
+  " journal = {Comp.~Phys.~Comm.},\n"
+  " year =    2008,\n"
+  " volume =  179,\n"
+  " pages =   {777--783}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_peri_package);
+
   molecular = 0;
 
   comm_x_only = 0;

src/POEMS/fix_poems.cpp

@@ -33,6 +33,7 @@
 #include "output.h"
 #include "group.h"
 #include "comm.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -45,6 +46,17 @@ using namespace FixConst;
 #define EPSILON 1.0e-7
 #define MAXJACOBI 50
 
+static const char cite_fix_poems[] =
+  "fix poems command:\n\n"
+  "@Article{Mukherjee08,\n"
+  " author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},\n"
+  " title = {Substructured molecular dynamics using multibody dynamics algorithms},\n"
+  " journal = {Intl.~J.~Non-linear Mechanics},\n"
+  " year =    2008,\n"
+  " volume =  43,\n"
+  " pages =   {1045--1055}\n"
+  "}\n\n";
+
 /* ----------------------------------------------------------------------
    define rigid bodies and joints, initiate POEMS
 ------------------------------------------------------------------------- */
@@ -52,6 +64,8 @@ using namespace FixConst;
 FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_poems);
+
   int i,j,ibody;
 
   time_integrate = 1;

src/SRD/fix_srd.cpp

@@ -37,6 +37,7 @@
 #include "random_mars.h"
 #include "random_park.h"
 #include "math_const.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -61,6 +62,17 @@ enum{NO_REMAP,X_REMAP,V_REMAP};                   // same as fix_deform.cpp
 #define TOLERANCE 0.00001
 #define MAXITER 20
 
+static const char cite_fix_srd[] =
+  "fix srd command:\n\n"
+  "@Article{Petersen10,\n"
+  " author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk},\n"
+  " title =   {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid},"
+  " journal = {J.~Chem.~Phys.},\n"
+  " year =    2010,\n"
+  " volume =  132,\n"
+  " pages =   {174106}\n"
+  "}\n\n";
+
 //#define SRD_DEBUG 1
 //#define SRD_DEBUG_ATOMID 58
 //#define SRD_DEBUG_TIMESTEP 449
@@ -69,6 +81,8 @@ enum{NO_REMAP,X_REMAP,V_REMAP};                   // same as fix_deform.cpp
 
 FixSRD::FixSRD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_srd);
+
   if (narg < 8) error->all(FLERR,"Illegal fix srd command");
 
   restart_pbc = 1;

src/USER-EFF/atom_vec_electron.cpp

@@ -24,6 +24,7 @@
 #include "modify.h"
 #include "force.h"
 #include "fix.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -31,10 +32,23 @@ using namespace LAMMPS_NS;
 
 #define DELTA 10000
 
+static const char cite_user_eff_package[] =
+  "USER-EFF package:\n\n"
+  "@Article{Jaramillo-Botero11,\n"
+  " author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n"
+  " title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},\n"
+  " journal = {J.~Comp.~Chem.},\n"
+  " year =    2011,\n"
+  " volume =  32,\n"
+  " pages =   {497--512}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_user_eff_package);
+
   comm_x_only = comm_f_only = 0;
 
   mass_type = 1;

src/USER-PHONON/fix_phonon.cpp

@@ -28,14 +28,15 @@
 #include "atom.h"
 #include "compute.h"
 #include "domain.h"
-#include "error.h"
 #include "fft3d_wrap.h"
 #include "force.h"
 #include "group.h"
 #include "lattice.h"
-#include "memory.h"
 #include "modify.h"
 #include "update.h"
+#include "citeme.h"
+#include "memory.h"
+#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -44,8 +45,23 @@ using namespace FixConst;
 #define INVOKED_VECTOR 2
 #define MAXLINE 256
 
+static const char cite_fix_phonon[] =
+  "fix phonon command:\n\n"
+  "@Article{Kong11,\n"
+  " author = {L. T. Kong},\n"
+  " title = {Phonon dispersion measured directly from molecular dynamics simulations},\n"
+  " journal = {Comp.~Phys.~Comm.},\n"
+  " year =    2011,\n"
+  " volume =  182,\n"
+  " pages =   {2201--2207}\n"
+  "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
 FixPhonon::FixPhonon(LAMMPS *lmp,  int narg, char **arg) : Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_phonon);
+
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);
   

src/USER-REAXC/fix_qeq_reax.cpp

@@ -14,11 +14,6 @@
 /* ----------------------------------------------------------------------
    Contributing author: Hasan Metin Aktulga, Purdue University
    (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
-
-   Please cite the related publication:
-   H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
-   "Parallel Reactive Molecular Dynamics: Numerical Methods and
-   Algorithmic Techniques", Parallel Computing, in press.
 ------------------------------------------------------------------------- */
 
 #include "math.h"
@@ -38,6 +33,7 @@
 #include "pair.h"
 #include "respa.h"
 #include "memory.h"
+#include "citeme.h"
 #include "error.h"
 #include "reaxc_defs.h"
 
@@ -51,11 +47,24 @@ using namespace FixConst;
 #define CUBE(x) ((x)*(x)*(x))
 #define MIN_NBRS 100
 
+static const char cite_fix_qeq_reax[] =
+  "fix qeq/reax command:\n\n"
+  "@Article{Aktulga12,\n"
+  " author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n"
+  " title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n"
+  " journal = {Parallel Computing},\n"
+  " year =    2012,\n"
+  " volume =  38,\n"
+  " pages =   {245--259}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_qeq_reax);
+
   if (narg != 8) error->all(FLERR,"Illegal fix qeq/reax command");
 
   nevery = force->inumeric(FLERR,arg[3]);

src/USER-REAXC/pair_reax_c.cpp

@@ -14,11 +14,6 @@
 /* ----------------------------------------------------------------------
    Contributing author: Hasan Metin Aktulga, Purdue University
    (now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
-   Please cite the related publication:
-   H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
-   "Parallel Reactive Molecular Dynamics: Numerical Methods and
-   Algorithmic Techniques", Parallel Computing, in press.
-   ---
    Per-atom energy/virial added by Ray Shan (Sandia)
    Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added by 
    	Ray Shan (Sandia)
@@ -35,6 +30,7 @@
 #include "modify.h"
 #include "fix.h"
 #include "fix_reax_c.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -54,10 +50,23 @@
 
 using namespace LAMMPS_NS;
 
+static const char cite_pair_reax_c[] =
+  "pair reax/c command:\n\n"
+  "@Article{Aktulga12,\n"
+  " author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n"
+  " title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n"
+  " journal = {Parallel Computing},\n"
+  " year =    2012,\n"
+  " volume =  38,\n"
+  " pages =   {245--259}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_pair_reax_c);
+
   single_enable = 0;
   restartinfo = 0;
   one_coeff = 1;

src/neighbor.cpp

@@ -54,7 +54,7 @@ enum{NSQ,BIN,MULTI};     // also in neigh_list.cpp
 
 static const char cite_neigh_multi[] =
   "neighbor multi command:\n\n"
-  "@Article{intveld08,\n"
+  "@Article{Intveld08,\n"
   " author =  {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
   " and G.{\\,}S.~Grest},\n"
   " title =   {Accurate and Efficient Methods for Modeling Colloidal\n"