From c612b724dfc3a7dd2f74c9313d3149be4fb27886 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 30 Jul 2013 20:40:02 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10492 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/ASPHERE/pair_gayberne.cpp | 14 ++++++++++++++ src/GPU/fix_gpu.cpp | 24 +++++++++++++++++++++++- src/MC/fix_bond_swap.cpp | 14 ++++++++++++++ src/MISC/fix_orient_fcc.cpp | 16 +++++++++++++++- src/PERI/atom_vec_peri.cpp | 14 ++++++++++++++ src/POEMS/fix_poems.cpp | 14 ++++++++++++++ src/SRD/fix_srd.cpp | 14 ++++++++++++++ src/USER-EFF/atom_vec_electron.cpp | 14 ++++++++++++++ src/USER-PHONON/fix_phonon.cpp | 20 ++++++++++++++++++-- src/USER-REAXC/fix_qeq_reax.cpp | 19 ++++++++++++++----- src/USER-REAXC/pair_reax_c.cpp | 19 ++++++++++++++----- src/neighbor.cpp | 2 +- 12 files changed, 169 insertions(+), 15 deletions(-) diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 4bc4cbc08c..f66aefd394 100755 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/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; } diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 44f4a5789d..6d9d2af6e0 100644 --- a/src/GPU/fix_gpu.cpp +++ b/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"); diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 2215d044eb..24474052f5 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/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; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index 3611478308..a7fc2eceaa 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/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"); diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index b4dbb37b94..9d8c6a74d4 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/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; diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 93296636be..599680f3d7 100644 --- a/src/POEMS/fix_poems.cpp +++ b/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; diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 68651cad12..01ff4e8f2a 100644 --- a/src/SRD/fix_srd.cpp +++ b/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; diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 565d63324c..e861414efb 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/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; diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index ee01f7258f..f8290d1720 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/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); diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 8ebf8fcfd5..d41e8f1543 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/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]); diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp index 4c1eea4f53..dd7c0e558e 100644 --- a/src/USER-REAXC/pair_reax_c.cpp +++ b/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; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 5a7c5312a2..b7329d7b0f 100644 --- a/src/neighbor.cpp +++ b/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"