| ewald | pppm | pppm/tip4p
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 5851a1ef14..9a625c4121 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -560,8 +560,11 @@ description:
:line
-Kspace solvers. All of these solver styles are discussed as part of
-the "kspace_style"_kspace_style.html command:
+Improper_style potentials.
+
+Kspace solvers. See the "kspace_style"_kspace_style.html command for
+an overview of Kspace solvers. Click on the style itself for a full
+description:
"ewald"_kspace_style.html,
"pppm"_kspace_style.html,
diff --git a/doc/Section_errors.html b/doc/Section_errors.html
index 62e66e3fbb..0487e1f4e9 100644
--- a/doc/Section_errors.html
+++ b/doc/Section_errors.html
@@ -3058,6 +3058,15 @@ lattice must first be defined via the lattice command.
If scale = lattice (the default) for the velocity set or velocity ramp
command, then a lattice must first be defined via the lattice command.
+Using fix nvt/sllod with inconsistent fix deform remap option
+
+Fix nvt/sllod requires that deforming atoms have a velocity profile
+provided by "remap v" as a fix deform option.
+
+Using fix nvt/sllod with no fix deform defined
+
+Self-explanatory.
+
Variable compute ID does not compute scalar info
The specified compute ID does not compute a scalar quantity
@@ -3360,15 +3369,6 @@ by "remap v" or "remap none" as a fix deform option.
Self-explanatory.
-Using fix nvt/sllod with inconsistent fix deform remap option
-
-Fix nvt/sllod assumes deforming atoms have a velocity profile
-provided by "remap v" as a fix deform option.
-
-Using fix nvt/sllod with no fix deform defined
-
-Self-explanatory.
-
Using pair tail corrections with nonperiodic system
This is probably a bogus thing to do, since tail corrections are
diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt
index cefe8641d4..b5e0f35452 100644
--- a/doc/Section_errors.txt
+++ b/doc/Section_errors.txt
@@ -3055,6 +3055,15 @@ lattice must first be defined via the lattice command. :dd
If scale = lattice (the default) for the velocity set or velocity ramp
command, then a lattice must first be defined via the lattice command. :dd
+{Using fix nvt/sllod with inconsistent fix deform remap option} :dt
+
+Fix nvt/sllod requires that deforming atoms have a velocity profile
+provided by "remap v" as a fix deform option. :dd
+
+{Using fix nvt/sllod with no fix deform defined} :dt
+
+Self-explanatory. :dd
+
{Variable compute ID does not compute scalar info} :dt
The specified compute ID does not compute a scalar quantity
@@ -3357,15 +3366,6 @@ by "remap v" or "remap none" as a fix deform option. :dd
Self-explanatory. :dd
-{Using fix nvt/sllod with inconsistent fix deform remap option} :dt
-
-Fix nvt/sllod assumes deforming atoms have a velocity profile
-provided by "remap v" as a fix deform option. :dd
-
-{Using fix nvt/sllod with no fix deform defined} :dt
-
-Self-explanatory. :dd
-
{Using pair tail corrections with nonperiodic system} :dt
This is probably a bogus thing to do, since tail corrections are
diff --git a/doc/Section_example.html b/doc/Section_example.html
index a7121fe407..20d68af123 100644
--- a/doc/Section_example.html
+++ b/doc/Section_example.html
@@ -23,20 +23,26 @@ the directories to compare your answers to. E.g. a log file like
log.crack.foo.P means it ran on P processors of machine "foo".
The dump files produced by the example runs can be animated using the
-xmovie tool described in the Tools section. MPEG
-versions of most of the xmovie animations are also viewable from the
-Examples page of the LAMMPS WWW Site.
+xmovie tool described in the Additional Tools
+section of the LAMMPS documentation. Animations of many of these
+examples can be viewed on the Movies section of the LAMMPS WWW
+Site.
These are the sample problems in the examples sub-directories:
-| crack | crack propagation in a 2d solid |
-| flow | Couette and Poiseuille flow in a 2d channel |
+| colloid | big colloid particles in a small particle solvent, 2d system |
+| crack | crack propagation in a 2d solid |
+| dipole | point dipolar particles, 2d system |
+| ellipse | ellipsoidal particles in spherical solvent, 2d system |
+| flow | Couette and Poisseuille flow in a 2d channel |
| friction | frictional contact of spherical asperities between 2d surfaces |
-| indent | spherical indenter into a 2d solid |
-| melt | rapid melt of 3d LJ system |
+| indent | spherical indenter into a 2d solid |
+| meam | MEAM test for SiC and shear (same as shear examples) |
+| melt | rapid melt of 3d LJ system |
| micelle | self-assembly of small lipid-like molecules into 2d bilayers |
-| min | energy minimization of 2d LJ melt |
+| min | energy minimization of 2d LJ melt |
+| nemd | non-equilibrium MD of 2d sheared system |
| obstacle | flow around two voids in a 2d channel |
| peptide | dynamics of a small solvated peptide chain (5-mer) |
| pour | pouring of granular particles into a 3d box, then chute flow |
diff --git a/doc/Section_example.txt b/doc/Section_example.txt
index 91b380e8fa..3db0d55d15 100644
--- a/doc/Section_example.txt
+++ b/doc/Section_example.txt
@@ -20,19 +20,25 @@ the directories to compare your answers to. E.g. a log file like
log.crack.foo.P means it ran on P processors of machine "foo".
The dump files produced by the example runs can be animated using the
-xmovie tool described in the "Tools section"_Section_tools.html. MPEG
-versions of most of the xmovie animations are also viewable from the
-Examples page of the "LAMMPS WWW Site"_lws.
+xmovie tool described in the "Additional Tools"_Section_tools.html
+section of the LAMMPS documentation. Animations of many of these
+examples can be viewed on the Movies section of the "LAMMPS WWW
+Site"_lws.
These are the sample problems in the examples sub-directories:
-crack: crack propagation in a 2d solid
-flow: Couette and Poiseuille flow in a 2d channel
+colloid: big colloid particles in a small particle solvent, 2d system
+crack: crack propagation in a 2d solid
+dipole: point dipolar particles, 2d system
+ellipse: ellipsoidal particles in spherical solvent, 2d system
+flow: Couette and Poisseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
-indent: spherical indenter into a 2d solid
-melt: rapid melt of 3d LJ system
+indent: spherical indenter into a 2d solid
+meam: MEAM test for SiC and shear (same as shear examples)
+melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers
-min: energy minimization of 2d LJ melt
+min: energy minimization of 2d LJ melt
+nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
pour: pouring of granular particles into a 3d box, then chute flow
diff --git a/doc/Section_history.html b/doc/Section_history.html
index 996c175d62..bced3bb538 100644
--- a/doc/Section_history.html
+++ b/doc/Section_history.html
@@ -33,11 +33,11 @@ time or interest; others are just a lot of work!
- Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS)
- torsional shear boundary conditions and temperature calculation
+
- NPT with changing box shape (Parinello-Rahman)
- bond creation potentials
-
- point dipole force fields
+
- long-range point dipole solver
- REBO bond-order potential
-
- ReaxFF force field from Bill Goddard's group
-
- Parinello-Rahman non-rectilinear simulation box
+
- ReaxFF force field from Bill Goddard's group
diff --git a/doc/Section_history.txt b/doc/Section_history.txt
index 2979a6cd01..4c576665cb 100644
--- a/doc/Section_history.txt
+++ b/doc/Section_history.txt
@@ -30,11 +30,11 @@ time or interest; others are just a lot of work!
Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS)
torsional shear boundary conditions and temperature calculation
+NPT with changing box shape (Parinello-Rahman)
bond creation potentials
-point dipole force fields
+long-range point dipole solver
REBO bond-order potential
-ReaxFF force field from Bill Goddard's group
-Parinello-Rahman non-rectilinear simulation box :ul
+ReaxFF force field from Bill Goddard's group :ul
:line
diff --git a/doc/Section_intro.html b/doc/Section_intro.html
index bbfd83cd43..a96e5e44ba 100644
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@@ -109,6 +109,8 @@ LAMMPS.
metals
granular materials
coarse-grained mesoscale models
+ ellipsoidal particles
+ point dipolar particles
hybrid systems
Force fields:
@@ -118,12 +120,15 @@ LAMMPS.
improper style, kspace style
commands)
-- pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), tabulated, hybrid
-
- manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), Stillinger-Weber, Tersoff
-
- bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable), hybrid
-
- angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS), hybrid
-
- dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS, hybrid
-
- improper potentials: harmonic, cvff, class 2 (COMPASS), hybrid
+
- pairwise potentials: Lennard-Jones, Buckingham, Morse, Yukawa, Debye, soft, class 2 (COMPASS), tabulated
+
- charged pairwise potentials: Coulombic, point-dipole
+
- manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), Stillinger-Weber, Tersoff
+
- coarse-grain potentials: granular, DPD, GayBerne, colloidal
+
- bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
+
- angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
+
- dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
+
- improper potentials: harmonic, cvff, class 2 (COMPASS)
+
- hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used
- polymer potentials: all-atom, united-atom, bead-spring, breakable
- water potentials: TIP3P, TIP4P, SPC
- long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)
@@ -144,10 +149,12 @@ commands)
(fix command)
-- constant NVE, NVT, NPT, NPH integrators
+
- 2d or 3d systems
+
- orthogonal or triclinic simulation domains
+
- constant NVE, NVT, NPT, NPH integrators
- thermostatting options for groups and geometric regions of atoms
- pressure control via Nose/Hoover barostatting in 1 to 3 dimensions
-
- volume rescaling
+
- simulation box deformation (tensile and shear)
- altered motion via velocity and force constraints
- harmonic (umbrella) constraint forces
- dragging of atoms to new positions
@@ -155,6 +162,7 @@ commands)
- SHAKE bond and angle constraints
- wall constraints of various kinds
- targeted molecular dynamics (TMD) constraints
+
- non-equilibrium molecular dynamics (NEMD)
- gravity
Integrators:
@@ -172,10 +180,12 @@ commands)
(dump, restart commands)
-- binary restart files
-
- text dump files of atom coords, velocities, other per-atom attributes
-
- atom snapshots in native, XYZ, XTC, DCD formats
-
- per-atom energy, stress, centro-symmetry parameter
+
- log file of thermodynanmic info
+
- text dump files of atom coords, velocities, other per-atom quantities
+
- binary restart files
+
- per-atom energy, stress, centro-symmetry parameter
+
- user-defined system-wide (log file) or per-atom (dump file) calculations
+
- atom snapshots in native, XYZ, XTC, DCD formats
Pre- and post-processing:
@@ -230,14 +240,14 @@ to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.
For atomic systems LAMMPS provides a create_atoms
-command which places atoms on solid-state lattices (fcc, bcc, etc).
-Assigning small numbers of force field coefficients can be done via
-the pair coeff, bond coeff, angle
-coeff, etc commands. For molecular systems or more
-complicated simulation geometries, users typically use another code as
-a builder and convert its output to LAMMPS input format, or write
-their own code to generate atom coordinate and molecular topology for
-LAMMPS to read in.
+command which places atoms on solid-state lattices (fcc, bcc,
+user-defined, etc). Assigning small numbers of force field
+coefficients can be done via the pair coeff, bond
+coeff, angle coeff, etc commands.
+For molecular systems or more complicated simulation geometries, users
+typically use another code as a builder and convert its output to
+LAMMPS input format, or write their own code to generate atom
+coordinate and molecular topology for LAMMPS to read in.
For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
@@ -251,12 +261,13 @@ section can assist in this process.
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
-LAMMPS runs, see this section for a discussion of how you
-can use the dump and fix commands to print out
-data of your choosing. Keep in mind that complicated computations can
-slow down the molecular dynamics timestepping, particularly if the
-computations are not parallel, so it is often better to leave such
-analysis to post-processing codes.
+LAMMPS runs, see this section for a discussion
+of how you can use the dump and compute and
+fix commands to print out data of your choosing. Keep in
+mind that complicated computations can slow down the molecular
+dynamics timestepping, particularly if the computations are not
+parallel, so it is often better to leave such analysis to
+post-processing codes.
A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the xmovie tool in this
@@ -265,10 +276,11 @@ atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
following packages:
-- Raster3d
-
- RasMol
-
- VMD
-
- AtomEye
+
Other features that LAMMPS does not yet (and may never) support are
discussed in this section.
@@ -441,55 +453,68 @@ features in LAMMPS:
+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)
+tensile and shear box deformations
+
-| 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)
+ | | NEMD SLLOD integration | Pieter in 't Veld (Sandia) |
+| pymol_asphere viz tool | Mike Brown (Sandia)
| 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 8d988d6927..ab35337250 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -105,6 +105,8 @@ Kinds of systems LAMMPS can simulate: :h4
metals
granular materials
coarse-grained mesoscale models
+ ellipsoidal particles
+ point dipolar particles
hybrid systems :ul
Force fields: :h4
@@ -113,18 +115,21 @@ Force fields: :h4
"improper style"_improper_style.html, "kspace style"_kspace_style.html
commands)
- pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, \
- Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), \
- tabulated, hybrid
- manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), \
+ pairwise potentials: Lennard-Jones, Buckingham, Morse, \
+ Yukawa, Debye, soft, class 2 (COMPASS), tabulated
+ charged pairwise potentials: Coulombic, point-dipole
+ manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
Stillinger-Weber, Tersoff
+ coarse-grain potentials: granular, DPD, GayBerne, colloidal
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
- quartic (breakable), hybrid
+ quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
- class 2 (COMPASS), hybrid
+ class 2 (COMPASS)
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
- class 2 (COMPASS), OPLS, hybrid
- improper potentials: harmonic, cvff, class 2 (COMPASS), hybrid
+ class 2 (COMPASS), OPLS
+ improper potentials: harmonic, cvff, class 2 (COMPASS)
+ hybrid potentials: multiple pair, bond, angle, dihedral, improper \
+ potentials can be used
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)
@@ -143,18 +148,19 @@ Creation of atoms: :h4
Ensembles, constraints, and boundary conditions: :h4
("fix"_fix.html command)
+ 2d or 3d systems
+ orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover barostatting in 1 to 3 dimensions
- volume rescaling
- altered motion via velocity and force constraints
+ simulation box deformation (tensile and shear)
harmonic (umbrella) constraint forces
- dragging of atoms to new positions
independent or coupled rigid body integration
SHAKE bond and angle constraints
- wall constraints of various kinds
+ walls of various kinds
targeted molecular dynamics (TMD) constraints
- gravity :ul
+ non-equilibrium molecular dynamics (NEMD)
+ variety of additional boundary conditions and constraints :ul
Integrators: :h4
("run"_run.html, "run_style"_run_style.html, "temper"_temper.html commands)
@@ -164,15 +170,17 @@ Integrators: :h4
energy minimization via conjugate gradient relaxation
rRESPA hierarchical timestepping
parallel tempering (replica exchange)
- multiple independent simulations simultaneously :ul
+ run multiple independent simulations simultaneously :ul
Output: :h4
("dump"_dump.html, "restart"_restart.html commands)
+ log file of thermodynanmic info
+ text dump files of atom coords, velocities, other per-atom quantities
binary restart files
- text dump files of atom coords, velocities, other per-atom attributes
- atom snapshots in native, XYZ, XTC, DCD formats
- per-atom energy, stress, centro-symmetry parameter :ul
+ per-atom energy, stress, centro-symmetry parameter
+ user-defined system-wide (log file) or per-atom (dump file) calculations
+ atom snapshots in native, XYZ, XTC, DCD formats :ul
Pre- and post-processing: :h4
@@ -226,14 +234,14 @@ to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.
For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
-command which places atoms on solid-state lattices (fcc, bcc, etc).
-Assigning small numbers of force field coefficients can be done via
-the "pair coeff"_pair_coeff.html, "bond coeff"_bond_coeff.html, "angle
-coeff"_angle_coeff.html, etc commands. For molecular systems or more
-complicated simulation geometries, users typically use another code as
-a builder and convert its output to LAMMPS input format, or write
-their own code to generate atom coordinate and molecular topology for
-LAMMPS to read in.
+command which places atoms on solid-state lattices (fcc, bcc,
+user-defined, etc). Assigning small numbers of force field
+coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
+coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
+For molecular systems or more complicated simulation geometries, users
+typically use another code as a builder and convert its output to
+LAMMPS input format, or write their own code to generate atom
+coordinate and molecular topology for LAMMPS to read in.
For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
@@ -247,12 +255,13 @@ Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
-LAMMPS runs, see "this section"_Section_modify.html for a discussion of how you
-can use the "dump"_dump.html and "fix"_fix.html commands to print out
-data of your choosing. Keep in mind that complicated computations can
-slow down the molecular dynamics timestepping, particularly if the
-computations are not parallel, so it is often better to leave such
-analysis to post-processing codes.
+LAMMPS runs, see "this section"_Section_modify.html for a discussion
+of how you can use the "dump"_dump.html and "compute"_compute.html and
+"fix"_fix.html commands to print out data of your choosing. Keep in
+mind that complicated computations can slow down the molecular
+dynamics timestepping, particularly if the computations are not
+parallel, so it is often better to leave such analysis to
+post-processing codes.
A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the "xmovie"_Section_tools.html#xmovie tool in "this
@@ -261,10 +270,11 @@ atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
following packages:
-"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
-"RasMol"_http://www.openrasmol.org
"VMD"_http://www.ks.uiuc.edu/Research/vmd
-"AtomEye"_http://164.107.79.177/Archive/Graphics/A :ul
+"AtomEye"_http://164.107.79.177/Archive/Graphics/A
+"PyMol"_http://pymol.sourceforge.net
+"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
+"RasMol"_http://www.openrasmol.org :ul
Other features that LAMMPS does not yet (and may never) support are
discussed in "this section"_Section_history.html.
@@ -479,7 +489,19 @@ 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) :tb(s=:)
+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)
+tensile and shear box deformations :
+NEMD SLLOD integration : Pieter in 't Veld (Sandia)
+pymol_asphere viz tool : Mike Brown (Sandia) :tb(s=:)
Other CRADA partners involved in the design and testing of LAMMPS were
diff --git a/doc/Section_start.html b/doc/Section_start.html
index 81428d0dca..07befc7297 100644
--- a/doc/Section_start.html
+++ b/doc/Section_start.html
@@ -274,9 +274,10 @@ can see the list of packages by typing "make package". The current
list of packages is as follows:
-| asphere | aspherical particles |
+| asphere | aspherical particles and force fields |
| class2 | class 2 force fields |
| colloid | colloidal particle force fields |
+| dipole | point dipole particles and force fields |
| dpd | dissipative particle dynamics (DPD) force field |
| granular | force fields and boundary conditions for granular systems |
| kspace | long-range Ewald and particle-mesh (PPPM) solvers |
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index 1c077d0d08..5a0794b4ba 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -268,9 +268,10 @@ fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
-asphere : aspherical particles
+asphere : aspherical particles and force fields
class2 : class 2 force fields
colloid : colloidal particle force fields
+dipole : point dipole particles and force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers
diff --git a/doc/Section_tools.html b/doc/Section_tools.html
index ab7457a059..af26153d36 100644
--- a/doc/Section_tools.html
+++ b/doc/Section_tools.html
@@ -54,7 +54,7 @@ own sub-directories with their own Makefiles.
- matlab
- micelle2d
- msi2lmp
-
- replicate
+
- pymol_asphere
- restart2data
- thermo_extract
- xmovie
@@ -227,17 +227,20 @@ experiment with it yourself.
-replicate tool
+pymol_asphere tool
-The file replicate.c takes a LAMMPS data file and replicates it into a
-larger system. The syntax for running the tool is
+ The pymol_asphere sub-directory contains a tool for converting a
+LAMMPS dump file that contains orientation info for ellipsoidal
+particles into an input file for the PyMol visualization
+package.
-replicate options < infile > outfile
-
-See the top of the replicate.c file for a discussion of the options.
-This tool is used by some of the LAMMPS benchmarks
-for creating larger systems to run scaled-size problems on multiple
-processors.
+
+
+ Specifically, the tool triangulates the ellipsoids so they can be
+viewed as true ellipsoidal particles within PyMol. See the README and
+examples directory within pymol_asphere for more information.
+
+This tool was written by Mike Brown at Sandia.
diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt
index 5c4f8bdecb..b43545441a 100644
--- a/doc/Section_tools.txt
+++ b/doc/Section_tools.txt
@@ -50,7 +50,7 @@ own sub-directories with their own Makefiles.
"matlab"_#matlab
"micelle2d"_#micelle
"msi2lmp"_#msi
-"replicate"_#replicate
+"pymol_asphere"_#pymol
"restart2data"_#restart
"thermo_extract"_#thermo_extract
"xmovie"_#xmovie :ul
@@ -223,17 +223,20 @@ experiment with it yourself.
:line
-replicate tool :h4,link(replicate)
+pymol_asphere tool :h4,link(pymol)
-The file replicate.c takes a LAMMPS data file and replicates it into a
-larger system. The syntax for running the tool is
+The pymol_asphere sub-directory contains a tool for converting a
+LAMMPS dump file that contains orientation info for ellipsoidal
+particles into an input file for the "PyMol visualization
+package"_pymol.
-replicate [options] < infile > outfile :pre
+:link(pymol,http://pymol.sourceforge.net)
-See the top of the replicate.c file for a discussion of the options.
-This tool is used by some of the "LAMMPS benchmarks"_Section_perf.html
-for creating larger systems to run scaled-size problems on multiple
-processors.
+Specifically, the tool triangulates the ellipsoids so they can be
+viewed as true ellipsoidal particles within PyMol. See the README and
+examples directory within pymol_asphere for more information.
+
+This tool was written by Mike Brown at Sandia.
:line
diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html
index 68d942e466..6d09b5e11e 100644
--- a/doc/compute_temp_deform.html
+++ b/doc/compute_temp_deform.html
@@ -20,7 +20,7 @@
Examples:
-compute myTemp all temp/deform myDeform
+compute myTemp all temp/deform
Description:
diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt
index 06cfdc6b88..0e192856b5 100644
--- a/doc/compute_temp_deform.txt
+++ b/doc/compute_temp_deform.txt
@@ -17,7 +17,7 @@ temp/deform = style name of this compute command :ul
[Examples:]
-compute myTemp all temp/deform myDeform :pre
+compute myTemp all temp/deform :pre
[Description:]
diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html
index 18a750009e..61dc955787 100644
--- a/doc/fix_nvt_sllod.html
+++ b/doc/fix_nvt_sllod.html
@@ -61,10 +61,10 @@ remapping either atom coordinates or velocities to the changing
simulation box. To use fix nvt/sllod, fix deform should NOT remap
atom positions, because fix nvt/sllod adjusts the atom positions and
velocities to create a velocity profile that matches the changing box
-size/shape. Fix deform SHOUDLD remap atom velocities when atoms cross
+size/shape. Fix deform SHOULD remap atom velocities when atoms cross
periodic boundaries since that is consistent with maintaining the
-velocity profile created by fix nvt/sllod. LAMMPS will warn you if
-this setting is not consistent.
+velocity profile created by fix nvt/sllod. LAMMPS will give an
+error if this setting is not consistent.
The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
discussed in (Tuckerman) (eqs 4 and 5), which is what is
diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt
index 821d212c95..d4896d9537 100644
--- a/doc/fix_nvt_sllod.txt
+++ b/doc/fix_nvt_sllod.txt
@@ -52,10 +52,10 @@ remapping either atom coordinates or velocities to the changing
simulation box. To use fix nvt/sllod, fix deform should NOT remap
atom positions, because fix nvt/sllod adjusts the atom positions and
velocities to create a velocity profile that matches the changing box
-size/shape. Fix deform SHOUDLD remap atom velocities when atoms cross
+size/shape. Fix deform SHOULD remap atom velocities when atoms cross
periodic boundaries since that is consistent with maintaining the
-velocity profile created by fix nvt/sllod. LAMMPS will warn you if
-this setting is not consistent.
+velocity profile created by fix nvt/sllod. LAMMPS will give an
+error if this setting is not consistent.
The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
diff --git a/doc/set.html b/doc/set.html
index 41ea98624f..93d1f85919 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -21,7 +21,7 @@
- one or more keyword/value pairs may be appended to the args
-
- keyword = type or type/fraction or mol or x or y or z or vx or vy or vz or charge or dipole or dipole/random or quat or quat/random or bond or angle or dihedral or improper
+
- keyword = type or type/fraction or mol or x or y or z or vx or vy or vz or charge or dipole or dipole/random or quat/random or bond or angle or dihedral or improper
type value = atom type
type/fraction values = type fraction seed
@@ -36,8 +36,9 @@
x,y,z = orientation of dipole moment vector
dipole/random value = seed
seed = random # seed (8 digits or less) for dipole moment orientations
- quat values = w i j k
- w,i,j,k = quaternion components (see below)
+ quat values = a b c theta
+ a,b,c = unit vector to rotate particle around via right-hand rule
+ theta = rotation angle in degrees
quat/random value = seed
seed = random # seed (8 digits or less) for quaternion orientations
bond value = bond type for all bonds between selected atoms
@@ -110,27 +111,30 @@ set by the dipole command.
Keyword dipole/random randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole
-moment for each atom is set by the dipole command.
-Random numbers are used in such a way that the orientation of a
-particular atom is the same, regardless of how many processors are
-being used.
+moment for each atom is set by the dipole command. For
+2d systems, the z component of the orientation is set to 0.0. Random
+numbers are used in such a way that the orientation of a particular
+atom is the same, regardless of how many processors are being used.
-Keyword quat uses the specified values as components of a quaternion
-(4-vector) to set the orientation of the selected atoms. Note that
-the shape command is used to specify the aspect ratios of
-an ellipsoidal particle, which is oriented by default with its x-axis
-along the simulation box's x-axis, and similarly for y and z. If this
-body is rotated (via the right-hand rule) by an angle theta around a
-unit vector (a,b,c), then the quaternion that represents its new
-orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
-c*sin(theta/2)). These 4 components are the arguments w,i,j,k to the
-quat keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
-not a unit vector.
+ Keyword quat uses the specified values to create a quaternion
+(4-vector) that represents the orientation of the selected atoms.
+Note that the shape command is used to specify the aspect
+ratios of an ellipsoidal particle, which is oriented by default with
+its x-axis along the simulation box's x-axis, and similarly for y and
+z. If this body is rotated (via the right-hand rule) by an angle
+theta around a unit rotation vector (a,b,c), then the quaternion that
+represents its new orientation is given by (cos(theta/2),
+a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
+values are the arguments to the quat keyword. LAMMPS normalizes the
+quaternion in case (a,b,c) was not specified as a unit vector. For 2d
+systems, the a,b,c values are ignored, since a rotation vector of
+(0,0,1) is the only valid choice.
Keyword quat/random randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
-processors are being used.
+processors are being used. For 2d systems, only orientations in the
+xy plane are generated.
For the dipole and quat keywords, the atom style
being used must support the use of dipoles or quaternions.
diff --git a/doc/set.txt b/doc/set.txt
index 6ee2c68f84..b3c011374a 100644
--- a/doc/set.txt
+++ b/doc/set.txt
@@ -17,8 +17,7 @@ ID = atom ID or group ID or region ID :l
one or more keyword/value pairs may be appended to the args :l
keyword = {type} or {type/fraction} or {mol} or \
{x} or {y} or {z} or {vx} or {vy} or {vz} or \
- {charge} or {dipole} or {dipole/random} or \
- {quat} or {quat/random} or \
+ {charge} or {dipole} or {dipole/random} or {quat/random} or \
{bond} or {angle} or {dihedral} or {improper} :l
{type} value = atom type
{type/fraction} values = type fraction seed
@@ -33,8 +32,9 @@ keyword = {type} or {type/fraction} or {mol} or \
x,y,z = orientation of dipole moment vector
{dipole/random} value = seed
seed = random # seed (8 digits or less) for dipole moment orientations
- {quat} values = w i j k
- w,i,j,k = quaternion components (see below)
+ {quat} values = a b c theta
+ a,b,c = unit vector to rotate particle around via right-hand rule
+ theta = rotation angle in degrees
{quat/random} value = seed
seed = random # seed (8 digits or less) for quaternion orientations
{bond} value = bond type for all bonds between selected atoms
@@ -106,27 +106,30 @@ set by the "dipole"_dipole.html command.
Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole
-moment for each atom is set by the "dipole"_dipole.html command.
-Random numbers are used in such a way that the orientation of a
-particular atom is the same, regardless of how many processors are
-being used.
+moment for each atom is set by the "dipole"_dipole.html command. For
+2d systems, the z component of the orientation is set to 0.0. Random
+numbers are used in such a way that the orientation of a particular
+atom is the same, regardless of how many processors are being used.
-Keyword {quat} uses the specified values as components of a quaternion
-(4-vector) to set the orientation of the selected atoms. Note that
-the "shape"_shape.html command is used to specify the aspect ratios of
-an ellipsoidal particle, which is oriented by default with its x-axis
-along the simulation box's x-axis, and similarly for y and z. If this
-body is rotated (via the right-hand rule) by an angle theta around a
-unit vector (a,b,c), then the quaternion that represents its new
-orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
-c*sin(theta/2)). These 4 components are the arguments w,i,j,k to the
-{quat} keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
-not a unit vector.
+Keyword {quat} uses the specified values to create a quaternion
+(4-vector) that represents the orientation of the selected atoms.
+Note that the "shape"_shape.html command is used to specify the aspect
+ratios of an ellipsoidal particle, which is oriented by default with
+its x-axis along the simulation box's x-axis, and similarly for y and
+z. If this body is rotated (via the right-hand rule) by an angle
+theta around a unit rotation vector (a,b,c), then the quaternion that
+represents its new orientation is given by (cos(theta/2),
+a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
+values are the arguments to the {quat} keyword. LAMMPS normalizes the
+quaternion in case (a,b,c) was not specified as a unit vector. For 2d
+systems, the a,b,c values are ignored, since a rotation vector of
+(0,0,1) is the only valid choice.
Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
-processors are being used.
+processors are being used. For 2d systems, only orientations in the
+xy plane are generated.
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
being used must support the use of dipoles or quaternions.
diff --git a/examples/README b/examples/README
index d1c981a88e..b13b37f00a 100644
--- a/examples/README
+++ b/examples/README
@@ -18,14 +18,18 @@ See the Errors section of the LAMMPS documentation for more
discussion.
The dump files produced by the example runs can be animated using the
-xmovie tool described in the Examples section of the LAMMPS
-documentation. MPEG versions of most of the xmovie animations are
-also viewable from the Examples section of the LAMMPS WWW Site.
+xmovie tool described in the "Additional Tools" section of the LAMMPS
+documentation. Animations of many of these examples can be viewed on
+the Movies section of the LAMMPS WWW Site.
These are the sample problems in the various sub-directories:
-couple: illustration of how to link to LAMMPS as a library
+couple: code example of how to link to LAMMPS as a library
+
+colloid: big colloid particles in a small particle solvent, 2d system
crack: crack propagation in a 2d solid
+dipole: point dipolar particles, 2d system
+ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poisseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
indent: spherical indenter into a 2d solid
@@ -33,6 +37,7 @@ meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
+nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
pour: pouring of granular particles into a 3d box, then chute flow
diff --git a/examples/couple/in.lj b/examples/couple/in.lj
index b8b4484da2..98de6750b4 100644
--- a/examples/couple/in.lj
+++ b/examples/couple/in.lj
@@ -7,7 +7,7 @@ atom_modify map array
lattice fcc 0.8442
region box block 0 4 0 4 0 4
create_box 1 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
diff --git a/examples/crack/in.crack b/examples/crack/in.crack
index eca4b83ab7..a17787a7b4 100644
--- a/examples/crack/in.crack
+++ b/examples/crack/in.crack
@@ -12,7 +12,7 @@ neigh_modify delay 5
lattice hex 0.93
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
mass 2 1.0
@@ -48,8 +48,8 @@ set group upper type 5
compute new mobile temp
velocity mobile create 0.01 887723 temp new
-velocity upper set 0.0 0.02 0.0
-velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
+velocity upper set 0.0 0.3 0.0
+velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
@@ -59,9 +59,9 @@ fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
-thermo 1000
+thermo 200
thermo_modify temp new
neigh_modify exclude type 2 3
-dump 1 all atom 250 dump.crack
-run 50000
+dump 1 all atom 500 dump.crack
+run 5000
diff --git a/examples/flow/in.flow.couette b/examples/flow/in.flow.couette
index 9ea023b162..542ce1eb79 100644
--- a/examples/flow/in.flow.couette
+++ b/examples/flow/in.flow.couette
@@ -12,7 +12,7 @@ neigh_modify delay 5
lattice hex 0.7
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
mass 2 1.0
diff --git a/examples/flow/in.flow.poiss b/examples/flow/in.flow.poiss
index 67ea6155a6..98de729533 100644
--- a/examples/flow/in.flow.poiss
+++ b/examples/flow/in.flow.poiss
@@ -12,7 +12,7 @@ neigh_modify delay 5
lattice hex 0.7
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
mass 2 1.0
diff --git a/examples/friction/in.friction b/examples/friction/in.friction
index 2d2f1be949..938c4f3bc2 100644
--- a/examples/friction/in.friction
+++ b/examples/friction/in.friction
@@ -76,5 +76,5 @@ timestep 0.0025
thermo 1000
thermo_modify temp new
-dump 1 all atom 100 dump.friction
+dump 1 all atom 500 dump.friction
run 20000
diff --git a/examples/indent/in.indent b/examples/indent/in.indent
index b7304ea88c..d65df80498 100644
--- a/examples/indent/in.indent
+++ b/examples/indent/in.indent
@@ -12,7 +12,7 @@ neigh_modify delay 5
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
mass 2 1.0
diff --git a/examples/indent/in.indent.min b/examples/indent/in.indent.min
index d22cb01a82..0dbb6d75eb 100644
--- a/examples/indent/in.indent.min
+++ b/examples/indent/in.indent.min
@@ -12,7 +12,7 @@ neigh_modify delay 5
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
-create_atoms 1
+create_atoms 1 box
mass * 1.0
@@ -40,7 +40,7 @@ fix 5 all enforce2d
thermo 10
-dump 1 all atom 10 dump.indent.min
+dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1000 1000
diff --git a/examples/meam/in.meam b/examples/meam/in.meam
index 43e83ea1ec..2c09d33159 100644
--- a/examples/meam/in.meam
+++ b/examples/meam/in.meam
@@ -8,7 +8,7 @@ atom_style atomic
read_data data.meam
pair_style meam
-pair_coeff * * library.meam Si C sic.meam Si C
+pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
diff --git a/examples/meam/in.meam.shear b/examples/meam/in.meam.shear
index 6f6d7c5b2e..c2aa510a13 100644
--- a/examples/meam/in.meam.shear
+++ b/examples/meam/in.meam.shear
@@ -10,10 +10,10 @@ create_box 3 box
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
origin 0.5 0 0
-create_atoms 1
+create_atoms 1 box
pair_style meam
-pair_coeff * * library.meam Ni4 ni.meam Ni4 Ni4 Ni4
+pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
@@ -62,7 +62,7 @@ unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
-dump 1 all atom 10 dump.meam.shear
+dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
diff --git a/examples/melt/in.melt b/examples/melt/in.melt
index aad27b8593..8367b1f3fe 100644
--- a/examples/melt/in.melt
+++ b/examples/melt/in.melt
@@ -4,9 +4,9 @@ units lj
atom_style atomic
lattice fcc 0.8442
-region box block 0 20 0 20 0 20
+region box block 0 10 0 10 0 10
create_box 1 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
@@ -19,7 +19,7 @@ neigh_modify every 20 delay 0 check no
fix 1 all nve
-dump id all atom 10 dump.melt
+dump id all atom 50 dump.melt
thermo 50
run 250
diff --git a/examples/micelle/in.micelle b/examples/micelle/in.micelle
index 642287e50c..5e4b6c4421 100644
--- a/examples/micelle/in.micelle
+++ b/examples/micelle/in.micelle
@@ -54,7 +54,7 @@ pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
-dump 1 all atom 250 dump.micelle
+dump 1 all atom 500 dump.micelle
reset_timestep 0
run 60000
diff --git a/examples/min/in.min b/examples/min/in.min
index e61291004b..0e1ab1f9c7 100644
--- a/examples/min/in.min
+++ b/examples/min/in.min
@@ -7,7 +7,7 @@ atom_style atomic
lattice sq2 0.8442
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
velocity all create 5.0 87287 loop geom
diff --git a/examples/obstacle/in.obstacle b/examples/obstacle/in.obstacle
index 1ac58b6f15..0c4b4fe5ab 100644
--- a/examples/obstacle/in.obstacle
+++ b/examples/obstacle/in.obstacle
@@ -12,7 +12,7 @@ neigh_modify delay 5
lattice hex 0.7
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
-create_atoms 1
+create_atoms 1 box
mass 1 1.0
mass 2 1.0
diff --git a/examples/pour/in.pour b/examples/pour/in.pour
index 55896c081f..11eb6c5a79 100644
--- a/examples/pour/in.pour
+++ b/examples/pour/in.pour
@@ -30,7 +30,7 @@ thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
-dump id all atom 125 dump.pour
+dump id all atom 1000 dump.pour
run 25000
unfix ins
diff --git a/examples/pour/in.pour.2d b/examples/pour/in.pour.2d
index af59539679..efefab6d4c 100644
--- a/examples/pour/in.pour.2d
+++ b/examples/pour/in.pour.2d
@@ -2,7 +2,7 @@
dimension 2
atom_style granular
-boundary p fm p
+boundary f fm p
newton off
region reg block 0 100 0 50 -0.5 0.5 units box
@@ -35,5 +35,5 @@ thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
-dump id all atom 100 dump.pour
+dump id all atom 250 dump.pour
run 25000
diff --git a/examples/shear/in.shear b/examples/shear/in.shear
index 6bcb801e99..828b867df9 100644
--- a/examples/shear/in.shear
+++ b/examples/shear/in.shear
@@ -10,10 +10,10 @@ create_box 3 box
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
origin 0.5 0 0
-create_atoms 1
+create_atoms 1 box
pair_style eam
-pair_coeff * * niu3.eam
+pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
@@ -62,7 +62,7 @@ unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
-dump 1 all atom 10 dump.shear
+dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
diff --git a/examples/shear/in.shear.void b/examples/shear/in.shear.void
index 8015249948..76f8eaba65 100644
--- a/examples/shear/in.shear.void
+++ b/examples/shear/in.shear.void
@@ -10,10 +10,10 @@ create_box 3 box
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
origin 0.5 0 0
-create_atoms 1
+create_atoms 1 box
pair_style eam
-pair_coeff * * niu3.eam
+pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
@@ -62,7 +62,7 @@ unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
-dump 1 all atom 10 dump.shear
+dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 5de299b889..71a9fefc23 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -399,6 +399,8 @@ double PairEAM::init_one(int i, int j)
} else if (setfl) cutmax = setfl->cut;
else if (fs) cutmax = fs->cut;
+ cutforcesq = cutmax*cutmax;
+
return cutmax;
}
@@ -412,8 +414,6 @@ void PairEAM::init_style()
file2array();
array2spline();
-
- cutforcesq = cutmax*cutmax;
}
/* ----------------------------------------------------------------------
diff --git a/src/Makefile.lib b/src/Makefile.lib
index 7aa15204e9..8a853a5129 100644
--- a/src/Makefile.lib
+++ b/src/Makefile.lib
@@ -7,9 +7,9 @@ SHELL = /bin/sh
ROOT = lmp
EXE = lib$(ROOT)_$@.a
-SRC = angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_dpd.cpp atom_vec_ellipsoid.cpp atom_vec_full.cpp atom_vec_granular.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_coord_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_asphere.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_variable.cpp compute_variable_atom.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xtc.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_com.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_npt_asphere.cpp fix_nve.cpp fix_nve_asphere.cpp fix_nve_gran.cpp fix_nve_noforce.cpp fix_nvt.cpp fix_nvt_asphere.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_pour.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_gran.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_alloy_opt.cpp pair_eam_fs.cpp pair_eam_fs_opt.cpp pair_eam_opt.cpp pair_gayberne.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_charmm_coul_long_opt.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_opt.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_morse_opt.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
+SRC = angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_dipole.cpp atom_vec_dpd.cpp atom_vec_ellipsoid.cpp atom_vec_full.cpp atom_vec_granular.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_coord_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_asphere.cpp compute_temp_deform.cpp compute_temp_dipole.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_variable.cpp compute_variable_atom.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xtc.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_com.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_npt_asphere.cpp fix_nve.cpp fix_nve_asphere.cpp fix_nve_dipole.cpp fix_nve_gran.cpp fix_nve_noforce.cpp fix_nvt.cpp fix_nvt_asphere.cpp fix_nvt_sllod.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_poems.cpp fix_pour.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_viscous.cpp fix_wall_gran.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_colloid.cpp pair_dipole_cut.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_alloy_opt.cpp pair_eam_fs.cpp pair_eam_fs_opt.cpp pair_eam_opt.cpp pair_gayberne.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_charmm_coul_long_opt.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_opt.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_meam.cpp pair_morse.cpp pair_morse_opt.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
-INC = angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_dpd.h atom_vec_ellipsoid.h atom_vec_full.h atom_vec_granular.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_coord_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_asphere.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h compute_variable.h compute_variable_atom.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xtc.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_ave_spatial.h fix_ave_time.h fix_com.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_heat.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_npt_asphere.h fix_nve.h fix_nve_asphere.h fix_nve_gran.h fix_nve_noforce.h fix_nvt.h fix_nvt_asphere.h fix_orient_fcc.h fix_plane_force.h fix_pour.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_gran.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h matho.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_alloy_opt.h pair_eam_fs.h pair_eam_fs_opt.h pair_eam_opt.h pair_gayberne.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_charmm_coul_long_opt.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_opt.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_morse_opt.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_asphere.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h vector.h velocity.h verlet.h write_restart.h
+INC = angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_dipole.h atom_vec_dpd.h atom_vec_ellipsoid.h atom_vec_full.h atom_vec_granular.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_coord_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_asphere.h compute_temp_deform.h compute_temp_dipole.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h compute_variable.h compute_variable_atom.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xtc.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_ave_spatial.h fix_ave_time.h fix_com.h fix_deform.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_heat.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_npt_asphere.h fix_nve.h fix_nve_asphere.h fix_nve_dipole.h fix_nve_gran.h fix_nve_noforce.h fix_nvt.h fix_nvt_asphere.h fix_nvt_sllod.h fix_orient_fcc.h fix_plane_force.h fix_poems.h fix_pour.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_viscous.h fix_wall_gran.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_colloid.h pair_dipole_cut.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_alloy_opt.h pair_eam_fs.h pair_eam_fs_opt.h pair_eam_opt.h pair_gayberne.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_charmm_coul_long_opt.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_opt.h pair_lj_expand.h pair_lj_smooth.h pair_meam.h pair_morse.h pair_morse_opt.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_asphere.h style_class2.h style_colloid.h style_dipole.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
OBJ = $(SRC:.cpp=.o)
diff --git a/src/Makefile.list b/src/Makefile.list
index 4030764979..4e0e437b0d 100644
--- a/src/Makefile.list
+++ b/src/Makefile.list
@@ -7,9 +7,9 @@ SHELL = /bin/sh
ROOT = lmp
EXE = $(ROOT)_$@
-SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_com.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_gravity.cpp fix_gyration.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_nve.cpp fix_nvt.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
+SRC = angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_dipole.cpp atom_vec_dpd.cpp atom_vec_ellipsoid.cpp atom_vec_full.cpp atom_vec_granular.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_coord_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_asphere.cpp compute_temp_deform.cpp compute_temp_dipole.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_variable.cpp compute_variable_atom.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xtc.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_com.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_npt_asphere.cpp fix_nve.cpp fix_nve_asphere.cpp fix_nve_dipole.cpp fix_nve_gran.cpp fix_nve_noforce.cpp fix_nvt.cpp fix_nvt_asphere.cpp fix_nvt_sllod.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_poems.cpp fix_pour.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_viscous.cpp fix_wall_gran.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_colloid.cpp pair_dipole_cut.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_alloy_opt.cpp pair_eam_fs.cpp pair_eam_fs_opt.cpp pair_eam_opt.cpp pair_gayberne.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_charmm_coul_long_opt.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_opt.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_meam.cpp pair_morse.cpp pair_morse_opt.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
-INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_com.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_gravity.h fix_gyration.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_nve.h fix_nvt.h fix_orient_fcc.h fix_plane_force.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
+INC = angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_dipole.h atom_vec_dpd.h atom_vec_ellipsoid.h atom_vec_full.h atom_vec_granular.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_coord_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_asphere.h compute_temp_deform.h compute_temp_dipole.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h compute_variable.h compute_variable_atom.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xtc.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_ave_spatial.h fix_ave_time.h fix_com.h fix_deform.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_heat.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_npt_asphere.h fix_nve.h fix_nve_asphere.h fix_nve_dipole.h fix_nve_gran.h fix_nve_noforce.h fix_nvt.h fix_nvt_asphere.h fix_nvt_sllod.h fix_orient_fcc.h fix_plane_force.h fix_poems.h fix_pour.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_viscous.h fix_wall_gran.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_colloid.h pair_dipole_cut.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_alloy_opt.h pair_eam_fs.h pair_eam_fs_opt.h pair_eam_opt.h pair_gayberne.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_charmm_coul_long_opt.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_opt.h pair_lj_expand.h pair_lj_smooth.h pair_meam.h pair_morse.h pair_morse_opt.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_asphere.h style_class2.h style_colloid.h style_dipole.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
OBJ = $(SRC:.cpp=.o)
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 52f8d16366..3afe22ddb6 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -56,8 +56,8 @@ void CreateAtoms::command(int narg, char **arg)
} else if (strcmp(arg[1],"region") == 0) {
style = REGION;
if (narg < 3) error->all("Illegal create_atoms command");
- int iregion = domain->find_region(arg[2]);
- if (iregion == -1) error->all("Create_atoms region ID does not exist");
+ nregion = domain->find_region(arg[2]);
+ if (nregion == -1) error->all("Create_atoms region ID does not exist");
iarg = 3;;
} else if (strcmp(arg[1],"single") == 0) {
style = SINGLE;
@@ -315,7 +315,7 @@ void CreateAtoms::add_many()
// if a region was specified, test if atom is in it
if (style == REGION)
- if (!domain->regions[iregion]->match(x[0],x[1],x[2])) continue;
+ if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
// test if atom is in my subbox
diff --git a/src/create_atoms.h b/src/create_atoms.h
index 38ced4e09b..db40d1d19c 100644
--- a/src/create_atoms.h
+++ b/src/create_atoms.h
@@ -24,7 +24,7 @@ class CreateAtoms : protected Pointers {
void command(int, char **);
private:
- int itype,style,iregion,nbasis;
+ int itype,style,nregion,nbasis;
int *basistype;
double xone[3];
diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp
index 758a0c74e7..fe39151532 100644
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@ -441,6 +441,7 @@ void FixAveSpatial::end_of_step()
for (i = 0; i < nvalues; i++) fprintf(fp," %g",values_total[m][i]);
fprintf(fp,"\n");
}
+ fflush(fp);
}
nsum = 0;
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 29a8f84f63..c0f1f15690 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -156,6 +156,7 @@ void FixAveTime::end_of_step()
if (vflag)
for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector[i]/nsum);
fprintf(fp,"\n");
+ fflush(fp);
}
nsum = 0;
diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp
index 4528203ad5..2f9818622c 100644
--- a/src/fix_nvt_sllod.cpp
+++ b/src/fix_nvt_sllod.cpp
@@ -23,7 +23,6 @@
#include "atom.h"
#include "force.h"
#include "domain.h"
-#include "comm.h"
#include "group.h"
#include "update.h"
#include "respa.h"
@@ -53,13 +52,12 @@ void FixNVTSlodd::init()
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP &&
- comm->me == 0)
- error->warning("Using fix nvt/sllod with inconsistent fix deform remap option");
+ if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ error->all("Using fix nvt/sllod with inconsistent fix deform remap option");
break;
}
- if (i == modify->nfix && comm->me == 0)
- error->warning("Using fix nvt/sllod with no fix deform defined");
+ if (i == modify->nfix)
+ error->all("Using fix nvt/sllod with no fix deform defined");
}
/* ---------------------------------------------------------------------- */
diff --git a/src/math_extra.h b/src/math_extra.h
index e043295681..5f4b268f86 100755
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -253,7 +253,7 @@ void MathExtra::mldivide3(const double m[3][3], const double *v, double *ans,
}
}
- while (aug[p][i] == 0 && p < 3) p++;
+ while (aug[p][i] == 0.0 && p < 3) p++;
if (p == 3) error->all("Bad matrix inversion in MathExtra::mldivide3");
else
@@ -270,7 +270,7 @@ void MathExtra::mldivide3(const double m[3][3], const double *v, double *ans,
}
}
- if (aug[2][2] == 0)
+ if (aug[2][2] == 0.0)
error->all("Bad matrix inversion in MathExtra::mldivide3");
// back substitution
diff --git a/src/style_meam.h b/src/style_meam.h
index e69de29bb2..221a363f11 100644
--- a/src/style_meam.h
+++ b/src/style_meam.h
@@ -0,0 +1,20 @@
+/* ----------------------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+#ifdef PairInclude
+#include "pair_meam.h"
+#endif
+
+#ifdef PairClass
+PairStyle(meam,PairMEAM)
+#endif
diff --git a/src/style_poems.h b/src/style_poems.h
index e69de29bb2..0434d02bf8 100644
--- a/src/style_poems.h
+++ b/src/style_poems.h
@@ -0,0 +1,20 @@
+/* ----------------------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+#ifdef FixInclude
+#include "fix_poems.h"
+#endif
+
+#ifdef FixClass
+FixStyle(poems,FixPOEMS)
+#endif
diff --git a/src/universe.cpp b/src/universe.cpp
index d0220999c3..2d1a9321a5 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp)
{
- version = "12 Feb 2007";
+ version = "22 June 2007";
uworld = communicator;
MPI_Comm_rank(uworld,&me);
diff --git a/tools/README b/tools/README
index ecccb7ef03..4f22ed919b 100644
--- a/tools/README
+++ b/tools/README
@@ -2,40 +2,33 @@ LAMMPS pre- and post-processing tools
This directory contains several stand-alone tools for creating LAMMPS
input files and massaging LAMMPS output data. Instructions on how to
-use the tools are discussed in the Tools section of the LAMMPS
-documentation. The source files in this directory have additional
-comments that may be useful at the top of the code. The packages that
-reside in their own sub-directories have README files of their own
-that you want to look at.
+use the tools are discussed in the "Additional Tools" section of the
+LAMMPS documentation.
-You will need to compile each of these tools if you wish to use them.
-Building LAMMPS itself (in the src dir) does not build these tools.
+Tools that are single source files in this directory have additional
+comments that may be useful at the top of the source file. Tools that
+reside in their own sub-directories have README files you should look
+at.
These are the included tools:
-binary2txt convert a LAMMPS dump file from binary to ASCII text
-replicate replicate a LAMMPS data file in one or more dimensions
-restart2data convert a binary restart file to an input data file
-data2xmovie convert a data file to a snapshot that xmovie can viz
-chain create a data file of bead-spring chains
-micelle2d create a data file of small lipid chains in solvent
-
-xmovie a quick/simple viz package that displays 2d projections
- of 3d LAMMPS snapshots
-
amber2lammps python scripts for using AMBER to setup LAMMPS input
+binary2txt convert a LAMMPS dump file from binary to ASCII text
ch2lmp convert CHARMM files to LAMMPS input
+chain create a data file of bead-spring chains
+data2xmovie convert a data file to a snapshot that xmovie can viz
lmp2arc convert LAMMPS output to Accelrys Insight format
- for analysis
-lmp2cfg convert LAMMPS output to CFG files that can be
- read by AtomEye visualizer
+lmp2cfg convert LAMMPS output to CFG files for AtomEye viz
lmp2traj convert LAMMPS output to contour, density profiles
-msi2lmp use the Accelrys Insight (nee MSI/Biosym Discover)
- code to setup LAMMPS input
+micelle2d create a data file of small lipid chains in solvent
+msi2lmp use Accelrys Insight code to setup LAMMPS input
+pymol_asphere convert LAMMPS output of ellipsoids to PyMol format
+restart2data convert a binary restart file to an input data file
+xmovie a quick/simple viz package (2d projections of 3d)
-The set of tools are single C, C++, or Fortran files. A Makefile for
-building them is included in this directory, but you will have to edit
-it for the compilers and paths on your system.
+For tools that are single C, C++, or Fortran files, a Makefile for
+building them is included in this directory. You may need to edit it
+for the compilers and paths on your system.
-The other tools are in their own sub-directories, and each has its own
-README file on how to build and use it.
+For tools in their own sub-directories, see their README file for info
+on how to build and use it.
diff --git a/tools/restart2data.cpp b/tools/restart2data.cpp
index 70e2431a22..055223bb06 100644
--- a/tools/restart2data.cpp
+++ b/tools/restart2data.cpp
@@ -366,7 +366,7 @@ main (int argc, char **argv)
void header(FILE *fp, Data &data)
{
- char *version = "12 Feb 2007";
+ char *version = "22 June 2007";
data.triclinic = 0;
|