LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. diff --git a/doc/Manual.pdf b/doc/Manual.pdf index 9b29026889..9c98a7afae 100644 Binary files a/doc/Manual.pdf and b/doc/Manual.pdf differ diff --git a/doc/Manual.txt b/doc/Manual.txt index 4d462b235a..0fe5ba2889 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -19,7 +19,7 @@ LAMMPS Documentation :c,h3 -(5 Oct 2007 version of LAMMPS) :c +(22 Jan 2008 version of LAMMPS) :c LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 0b098c1fdc..9c1bf3d170 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -1360,6 +1360,10 @@ value.
Here are various folks who have made significant contributions to -features in LAMMPS: +features in LAMMPS. The most recent contributions are at the top of +the list.
| Ewald and PPPM solvers | Roy Pollock (LLNL) | |
| rRESPA | Mark Stevens & Paul Crozier (Sandia) | |
| NVT/NPT integrators | Mark Stevens (Sandia) | |
| class 2 force fields | Eric Simon (Cray) | |
| HTFN energy minimizer | Todd Plantenga (Sandia) | |
| msi2lmp tool | Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray) | |
| CHARMM force fields | Paul Crozier (Sandia) | |
| 2d Ewald/PPPM | Paul Crozier (Sandia) | |
| granular force fields and BC | Leo Silbert & Gary Grest (Sandia) | |
| multi-harmonic dihedral potential | Mathias Putz (Sandia) | |
| EAM potentials | Stephen Foiles (Sandia) | |
| parallel tempering | Mark Sears (Sandia) | |
| lmp2cfg and lmp2traj tools | Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia) | |
| FFT support for SGI SCLS (Altix) | Jim Shepherd (Ga Tech) | |
| targeted molecular dynamics (TMD) | Paul Crozier (Sandia), Christian Burisch (Bochum University, Germany) | |
| force tables for long-range Coulombics | Paul Crozier (Sandia) | |
| radial distribution functions | Paul Crozier & Jeff Greathouse (Sandia) | |
| Morse bond potential | Jeff Greathouse (Sandia) | |
| CHARMM <-> LAMMPS tool | Pieter in't Veld and Paul Crozier (Sandia) | |
| AMBER <-> LAMMPS tool | Keir Novik (Univ College London) and Vikas Varshney (U Akron) | |
| electric field fix | Christina Payne (Vanderbilt U) | |
| cylindrical indenter fix | Ravi Agrawal (Northwestern U) | |
| compressed dump files | Erik Luijten (U Illinois) | |
| thermodynamics enhanced by fix quantities | Aidan Thompson (Sandia) | |
| uniaxial strain fix | Carsten Svaneborg (Max Planck Institute) | |
| TIP4P potential (4-site water) | Ahmed Ismail and Amalie Frischknecht (Sandia) | |
| dissipative particle dynamics (DPD) potentials | Kurt Smith (U Pitt) and Frank van Swol (Sandia) | |
| Finnis/Sinclair EAM | Tim Lau (MIT) | |
| helix dihedral potential | Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia) | |
| cosine/squared angle potential | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| EAM CoAl and AlCu potentials | Kwang-Reoul Lee (KIST, Korea) | |
| self spring fix | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| radius-of-gyration spring fix | Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia) | |
| lj/smooth pair potential | Craig Maloney (UCSB) | |
| grain boundary orientation fix | Koenraad Janssens and David Olmsted (SNL) | |
| DCD and XTC dump styles | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| breakable bond quartic potential | Chris Lorenz and Mark Stevens (SNL) | |
| faster pair hybrid potential | James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology) | |
| POEMS coupled rigid body integrator | Rudranarayan Mukherjee (RPI) | |
| OPLS dihedral potential | Mark Stevens (Sandia) | |
| multi-letter variable names | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| fix momentum and recenter | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| LJ tail corrections for energy/pressure | Paul Crozier (Sandia) | |
| region prism | Pieter in't Veld (Sandia) | |
| Stillinger-Weber and Tersoff potentials | Aidan Thompson (Sandia) | |
| fix wall/lj126 | Mark Stevens (Sandia) | |
| optimized pair potentials for lj/cut, charmm/long, eam, morse | James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies) | |
| MEAM potential | Greg Wagner (Sandia) | |
| fix ave/time and fix ave/spatial | Pieter in 't Veld (Sandia) | |
| thermo_extract tool | Vikas Varshney (Wright Patterson AFB) | |
| triclinic (non-orthogonal) simulation domains | Pieter in 't Veld (Sandia) | |
| MATLAB post-processing scripts | Arun Subramaniyan (Purdue) | |
| neighbor multi and communicate multi | Pieter in 't Veld (Sandia) | |
| fix heat | Paul Crozier and Ed Webb (Sandia) | |
| colloid potentials | Pieter in 't Veld (Sandia) | |
| ellipsoidal particles | Mike Brown (Sandia) | |
| GayBerne potential | Mike Brown (Sandia) | |
| fix deform | Pieter in 't Veld (Sandia) | |
| VIM editor add-ons for LAMMPS input scripts | Gerolf Ziegenhain | |
| pair lubricate | Randy Schunk (Sandia) | |
| compute ackland/atom | Gerolf Zeigenhain | |
| kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul | Pieter in 't Veld (Sandia) | |
| AI-REBO bond-order potential | Ase Henry (MIT) | |
| making LAMMPS a true "object" that can be instantiated multiple times, e.g. as a library | Ben FrantzDale (RPI) | |
| pymol_asphere viz tool | Mike Brown (Sandia) | |
| NEMD SLLOD integration | Pieter in 't Veld (Sandia) | |
| pymol_asphere viz tool | Mike Brown (Sandia) + | |
| tensile and shear deformations | Pieter in 't Veld (Sandia) | |
| GayBerne potential | Mike Brown (Sandia) | |
| ellipsoidal particles | Mike Brown (Sandia) | |
| colloid potentials | Pieter in 't Veld (Sandia) | |
| fix heat | Paul Crozier and Ed Webb (Sandia) | |
| neighbor multi and communicate multi | Pieter in 't Veld (Sandia) | |
| MATLAB post-processing scripts | Arun Subramaniyan (Purdue) | |
| triclinic (non-orthogonal) simulation domains | Pieter in 't Veld (Sandia) | |
| thermo_extract tool | Vikas Varshney (Wright Patterson AFB) | |
| fix ave/time and fix ave/spatial | Pieter in 't Veld (Sandia) | |
| MEAM potential | Greg Wagner (Sandia) | |
| optimized pair potentials for lj/cut, charmm/long, eam, morse | James Fischer (High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies) | |
| fix wall/lj126 | Mark Stevens (Sandia) | |
| Stillinger-Weber and Tersoff potentials | Aidan Thompson (Sandia) | |
| region prism | Pieter in 't Veld (Sandia) | |
| LJ tail corrections for energy/pressure | Paul Crozier (Sandia) | |
| fix momentum and recenter | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| multi-letter variable names | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| OPLS dihedral potential | Mark Stevens (Sandia) | |
| POEMS coupled rigid body integrator | Rudranarayan Mukherjee (RPI) | |
| faster pair hybrid potential | James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology) | |
| breakable bond quartic potential | Chris Lorenz and Mark Stevens (Sandia) | |
| DCD and XTC dump styles | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| grain boundary orientation fix | Koenraad Janssens and David Olmsted (Sandia) | |
| lj/smooth pair potential | Craig Maloney (UCSB) | |
| radius-of-gyration spring fix | Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia) | |
| self spring fix | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| EAM CoAl and AlCu potentials | Kwang-Reoul Lee (KIST, Korea) | |
| cosine/squared angle potential | Naveen Michaud-Agrawal (Johns Hopkins U) | |
| helix dihedral potential | Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia) | |
| Finnis/Sinclair EAM | Tim Lau (MIT) | |
| dissipative particle dynamics (DPD) potentials | Kurt Smith (U Pitt) and Frank van Swol (Sandia) | |
| TIP4P potential (4-site water) | Ahmed Ismail and Amalie Frischknecht (Sandia) | |
| uniaxial strain fix | Carsten Svaneborg (Max Planck Institute) | |
| thermodynamics enhanced by fix quantities | Aidan Thompson (Sandia) | |
| compressed dump files | Erik Luijten (U Illinois) | |
| cylindrical indenter fix | Ravi Agrawal (Northwestern U) | |
| electric field fix | Christina Payne (Vanderbilt U) | |
| AMBER <-> LAMMPS tool | Keir Novik (Univ College London) and Vikas Varshney (U Akron) | |
| CHARMM <-> LAMMPS tool | Pieter in 't Veld and Paul Crozier (Sandia) | |
| Morse bond potential | Jeff Greathouse (Sandia) | |
| radial distribution functions | Paul Crozier & Jeff Greathouse (Sandia) | |
| force tables for long-range Coulombics | Paul Crozier (Sandia) | |
| targeted molecular dynamics (TMD) | Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany) | |
| FFT support for SGI SCLS (Altix) | Jim Shepherd (Ga Tech) | |
| lmp2cfg and lmp2traj tools | Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia) | |
| parallel tempering | Mark Sears (Sandia) | |
| embedded atom method (EAM) potential | Stephen Foiles (Sandia) | |
| multi-harmonic dihedral potential | Mathias Putz (Sandia) | |
| granular force fields and BC | Leo Silbert & Gary Grest (Sandia) | |
| 2d Ewald/PPPM | Paul Crozier (Sandia) | |
| CHARMM force fields | Paul Crozier (Sandia) | |
| msi2lmp tool | Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray) | |
| HTFN energy minimizer | Todd Plantenga (Sandia) | |
| class 2 force fields | Eric Simon (Cray) | |
| NVT/NPT integrators | Mark Stevens (Sandia) | |
| rRESPA | Mark Stevens & Paul Crozier (Sandia) | |
| Ewald and PPPM solvers | Roy Pollock (LLNL) |
Other CRADA partners involved in the design and testing of LAMMPS were diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 9f8cea01a1..feece7de40 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -436,75 +436,89 @@ include "Steve Plimpton"_sjp, Paul Crozier, and Aidan Thompson and can be contacted via email: sjplimp, pscrozi, athomps at sandia.gov. Here are various folks who have made significant contributions to -features in LAMMPS: +features in LAMMPS. The most recent contributions are at the top of +the list. :link(sjp,http://www.cs.sandia.gov/~sjplimp) -Ewald and PPPM solvers: Roy Pollock (LLNL) -rRESPA: Mark Stevens & Paul Crozier (Sandia) -NVT/NPT integrators: Mark Stevens (Sandia) -class 2 force fields: Eric Simon (Cray) -HTFN energy minimizer: Todd Plantenga (Sandia) -msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray) -CHARMM force fields: Paul Crozier (Sandia) -2d Ewald/PPPM: Paul Crozier (Sandia) -granular force fields and BC: Leo Silbert & Gary Grest (Sandia) -multi-harmonic dihedral potential: Mathias Putz (Sandia) -EAM potentials: Stephen Foiles (Sandia) -parallel tempering: Mark Sears (Sandia) -lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia) -FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech) -targeted molecular dynamics (TMD): Paul Crozier (Sandia), Christian Burisch (Bochum University, Germany) -force tables for long-range Coulombics: Paul Crozier (Sandia) -radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia) -Morse bond potential: Jeff Greathouse (Sandia) -CHARMM <-> LAMMPS tool: Pieter in't Veld and Paul Crozier (Sandia) -AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and Vikas Varshney (U Akron) -electric field fix: Christina Payne (Vanderbilt U) -cylindrical indenter fix: Ravi Agrawal (Northwestern U) -compressed dump files: Erik Luijten (U Illinois) -thermodynamics enhanced by fix quantities: Aidan Thompson (Sandia) -uniaxial strain fix: Carsten Svaneborg (Max Planck Institute) -TIP4P potential (4-site water): Ahmed Ismail and Amalie Frischknecht (Sandia) -dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \ - Frank van Swol (Sandia) -Finnis/Sinclair EAM: Tim Lau (MIT) -helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \ - Mark Stevens (Sandia) -cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U) -EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea) -self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) -radius-of-gyration spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) and \ - Paul Crozier (Sandia) -lj/smooth pair potential : Craig Maloney (UCSB) -grain boundary orientation fix : Koenraad Janssens and David Olmsted (SNL) -DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U) -breakable bond quartic potential: Chris Lorenz and Mark Stevens (SNL) +VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain +pair lubricate : Randy Schunk (Sandia) +compute ackland/atom : Gerolf Zeigenhain +kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \ + Pieter in 't Veld (Sandia) +AI-REBO bond-order potential : Ase Henry (MIT) +making LAMMPS a true "object" that can be instantiated multiple times, \ + e.g. as a library : Ben FrantzDale (RPI) +pymol_asphere viz tool : Mike Brown (Sandia) +NEMD SLLOD integration : Pieter in 't Veld (Sandia) +tensile and shear deformations : Pieter in 't Veld (Sandia) +GayBerne potential : Mike Brown (Sandia) +ellipsoidal particles : Mike Brown (Sandia) +colloid potentials : Pieter in 't Veld (Sandia) +fix heat : Paul Crozier and Ed Webb (Sandia) +neighbor multi and communicate multi : Pieter in 't Veld (Sandia) +MATLAB post-processing scripts : Arun Subramaniyan (Purdue) +triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia) +thermo_extract tool: Vikas Varshney (Wright Patterson AFB) +fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia) +MEAM potential : Greg Wagner (Sandia) +optimized pair potentials for lj/cut, charmm/long, eam, morse : \ + James Fischer (High Performance Technologies), \ + David Richie and Vincent Natoli (Stone Ridge Technologies) +fix wall/lj126 : Mark Stevens (Sandia) +Stillinger-Weber and Tersoff potentials : Aidan Thompson (Sandia) +region prism : Pieter in 't Veld (Sandia) +LJ tail corrections for energy/pressure : Paul Crozier (Sandia) +fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U) +multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U) +OPLS dihedral potential: Mark Stevens (Sandia) +POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI) faster pair hybrid potential: James Fischer \ (High Performance Technologies, Inc), Vincent Natoli and \ David Richie (Stone Ridge Technology) -POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI) -OPLS dihedral potential: Mark Stevens (Sandia) -multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U) -fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U) -LJ tail corrections for energy/pressure : Paul Crozier (Sandia) -region prism : Pieter in't Veld (Sandia) -Stillinger-Weber and Tersoff potentials : Aidan Thompson (Sandia) -fix wall/lj126 : Mark Stevens (Sandia) -optimized pair potentials for lj/cut, charmm/long, eam, morse : James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies) -MEAM potential : Greg Wagner (Sandia) -fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia) -thermo_extract tool: Vikas Varshney (Wright Patterson AFB) -triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia) -MATLAB post-processing scripts : Arun Subramaniyan (Purdue) -neighbor multi and communicate multi : Pieter in 't Veld (Sandia) -fix heat : Paul Crozier and Ed Webb (Sandia) -colloid potentials : Pieter in 't Veld (Sandia) -ellipsoidal particles : Mike Brown (Sandia) -GayBerne potential : Mike Brown (Sandia) -fix deform : Pieter in 't Veld (Sandia) -NEMD SLLOD integration : Pieter in 't Veld (Sandia) -pymol_asphere viz tool : Mike Brown (Sandia) :tb(s=:) +breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia) +DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U) +grain boundary orientation fix : Koenraad Janssens and David Olmsted (Sandia) +lj/smooth pair potential : Craig Maloney (UCSB) +radius-of-gyration spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) and \ + Paul Crozier (Sandia) +self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) +EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea) +cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U) +helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \ + Mark Stevens (Sandia) +Finnis/Sinclair EAM: Tim Lau (MIT) +dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \ + Frank van Swol (Sandia) +TIP4P potential (4-site water): Ahmed Ismail and Amalie Frischknecht (Sandia) +uniaxial strain fix: Carsten Svaneborg (Max Planck Institute) +thermodynamics enhanced by fix quantities: Aidan Thompson (Sandia) +compressed dump files: Erik Luijten (U Illinois) +cylindrical indenter fix: Ravi Agrawal (Northwestern U) +electric field fix: Christina Payne (Vanderbilt U) +AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \ + Vikas Varshney (U Akron) +CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia) +Morse bond potential: Jeff Greathouse (Sandia) +radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia) +force tables for long-range Coulombics: Paul Crozier (Sandia) +targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \ + Christian Burisch (Bochum University, Germany) +FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech) +lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \ + Andrey Kalinichev (Sandia) +parallel tempering: Mark Sears (Sandia) +embedded atom method (EAM) potential: Stephen Foiles (Sandia) +multi-harmonic dihedral potential: Mathias Putz (Sandia) +granular force fields and BC: Leo Silbert & Gary Grest (Sandia) +2d Ewald/PPPM: Paul Crozier (Sandia) +CHARMM force fields: Paul Crozier (Sandia) +msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray) +HTFN energy minimizer: Todd Plantenga (Sandia) +class 2 force fields: Eric Simon (Cray) +NVT/NPT integrators: Mark Stevens (Sandia) +rRESPA: Mark Stevens & Paul Crozier (Sandia) +Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:) Other CRADA partners involved in the design and testing of LAMMPS were