From d17e06c479e961879a1c3b0a3ba5cefa2e5c1121 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 13 May 2014 14:04:47 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11976 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html.html | 266 ------------------- doc/Section_commands.html | 31 +-- doc/Section_commands.txt | 5 +- doc/balance.html | 282 +++++++++++++-------- doc/balance.txt | 279 ++++++++++++-------- doc/{communicate.html => comm_modify.html} | 57 +++-- doc/{communicate.txt => comm_modify.txt} | 54 ++-- doc/comm_style.html | 70 +++++ doc/comm_style.txt | 65 +++++ doc/create_box.html | 22 +- doc/create_box.txt | 22 +- doc/fix_balance.html | 243 +++++++++++------- doc/fix_balance.txt | 241 +++++++++++------- doc/processors.html | 51 ++-- doc/processors.txt | 51 ++-- doc/read_data.html | 7 +- doc/read_data.txt | 7 +- doc/read_restart.html | 10 +- doc/read_restart.txt | 10 +- doc/replicate.html | 7 +- doc/replicate.txt | 7 +- 21 files changed, 1009 insertions(+), 778 deletions(-) delete mode 100644 doc/Manual.html.html rename doc/{communicate.html => comm_modify.html} (73%) rename doc/{communicate.txt => comm_modify.txt} (73%) create mode 100644 doc/comm_style.html create mode 100644 doc/comm_style.txt diff --git a/doc/Manual.html.html b/doc/Manual.html.html deleted file mode 100644 index 72aee7a66c..0000000000 --- a/doc/Manual.html.html +++ /dev/null @@ -1,266 +0,0 @@ - - - -LAMMPS Users Manual - - - - - - - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- -
- -

- -

LAMMPS Documentation -

-

10 May 2014 version -

-

Version info: -

-

The LAMMPS "version" is the date when it was released, such as 1 May -2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of -the WWW site. Each dated copy of LAMMPS contains all the -features and bug-fixes up to and including that version date. The -version date is printed to the screen and logfile every time you run -LAMMPS. It is also in the file src/version.h and in the LAMMPS -directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). -

- -

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. -

-

LAMMPS is a classical molecular dynamics simulation code designed to -run efficiently on parallel computers. It was developed at Sandia -National Laboratories, a US Department of Energy facility, with -funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). -

-

The primary developers of LAMMPS are Steve Plimpton, Aidan -Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses. -

- -
- -

The LAMMPS documentation is organized into the following sections. If -you find errors or omissions in this manual or have suggestions for -useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. -

-

Once you are familiar with LAMMPS, you may want to bookmark this -page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. -

-

PDF file of the entire manual, generated by -htmldoc -

-
  1. Introduction - - -
  2. Getting started - - -
  3. Commands - - -
  4. Packages - - -
  5. Accelerating LAMMPS performance - - -
  6. How-to discussions - - -
  7. Example problems - -
  8. Performance & scalability - -
  9. Additional tools - -
  10. Modifying & extending LAMMPS - - -
  11. Python interface - - -
  12. Errors - - -
  13. Future and history - - - -
- - - - - - diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 0888116918..229de6b9da 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -309,7 +309,7 @@ in the command's documentation.

Settings:

-

communicate, group, mass, +

comm_style, group, mass, min_modify, min_style, neigh_modify, neighbor, reset_timestep, run_style, @@ -362,20 +362,21 @@ in the command's documentation.

- - - - - - - - - - - - - - + + + + + + + + + + + + + +
angle_coeffangle_styleatom_modifyatom_stylebalancebond_coeff
bond_styleboundaryboxchange_boxclearcommunicate
computecompute_modifycreate_atomscreate_boxdelete_atomsdelete_bonds
dielectricdihedral_coeffdihedral_styledimensiondisplace_atomsdump
dump imagedump_modifydump movieechofixfix_modify
groupifimproper_coeffimproper_styleincludejump
kspace_modifykspace_stylelabellatticelogmass
minimizemin_modifymin_stylemoleculenebneigh_modify
neighbornewtonnextpackagepair_coeffpair_modify
pair_stylepair_writepartitionprdprintprocessors
quitread_dataread_dumpread_restartregionreplicate
rerunreset_timesteprestartrunrun_styleset
shellspecial_bondssuffixtadtemperthermo
thermo_modifythermo_styletimestepuncomputeundumpunfix
unitsvariablevelocitywrite_datawrite_dumpwrite_restart +
bond_styleboundaryboxchange_boxclearcomm_modify
comm_stylecomputecompute_modifycreate_atomscreate_boxdelete_atoms
delete_bondsdielectricdihedral_coeffdihedral_styledimensiondisplace_atoms
dumpdump imagedump_modifydump movieechofix
fix_modifygroupifimproper_coeffimproper_styleinclude
jumpkspace_modifykspace_stylelabellatticelog
massminimizemin_modifymin_stylemoleculeneb
neigh_modifyneighbornewtonnextpackagepair_coeff
pair_modifypair_stylepair_writepartitionprdprint
processorsquitread_dataread_dumpread_restartregion
replicatererunreset_timesteprestartrunrun_style
setshellspecial_bondssuffixtadtemper
thermothermo_modifythermo_styletimestepuncomputeundump
unfixunitsvariablevelocitywrite_datawrite_dump
write_restart

These are commands contributed by users, which can be used if LAMMPS diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index c9acfcd8f4..133972811f 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -305,7 +305,7 @@ Force fields: Settings: -"communicate"_communicate.html, "group"_group.html, "mass"_mass.html, +"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, @@ -367,7 +367,8 @@ in the command's documentation. "box"_box.html, "change_box"_change_box.html, "clear"_clear.html, -"communicate"_communicate.html, +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, "compute"_compute.html, "compute_modify"_compute_modify.html, "create_atoms"_create_atoms.html, diff --git a/doc/balance.html b/doc/balance.html index 94088e0e01..22ffe25648 100644 --- a/doc/balance.html +++ b/doc/balance.html @@ -13,111 +13,178 @@

Syntax:

-
balance keyword args ... 
+
balance thresh style args keyword value ... 
 

-
 
The initial simulation box size is determined by the lo/hi settings.
 In any dimension, the system may be periodic or non-periodic; see the
-boundary command.
+boundary command.  When the simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the processors command.  The
+partitioning can later be changed by the balance or
+fix balance commands.
 

 
If the xy xz yz line does not appear, LAMMPS will set up an
 axis-aligned (orthogonal) simulation box.  If the line does appear,
diff --git a/doc/read_data.txt b/doc/read_data.txt
index 4ff5159bf8..b3d35d22cc 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -114,7 +114,12 @@ is different than the default.
 
 The initial simulation box size is determined by the lo/hi settings.
 In any dimension, the system may be periodic or non-periodic; see the
-"boundary"_boundary.html command.
+"boundary"_boundary.html command.  When the simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the "processors"_processors.html command.  The
+partitioning can later be changed by the "balance"_balance.html or
+"fix balance"_fix_balance.html commands.
 
 If the {xy xz yz} line does not appear, LAMMPS will set up an
 axis-aligned (orthogonal) simulation box.  If the line does appear,
diff --git a/doc/read_restart.html b/doc/read_restart.html
index 2966ba78e0..4835373854 100644
--- a/doc/read_restart.html
+++ b/doc/read_restart.html
@@ -30,7 +30,15 @@ read_restart poly.*.%
 

 
Read in a previously saved simulation from a restart file.  This
 allows continuation of a previous run.  Information about what is
-stored in a restart file is given below.
+stored in a restart file is given below.  Basically this operation
+will re-create the simulation box with all its atoms and their
+attributes, at the point in time it was written to the restart file by
+a previous simluation.  The simulation box will be partitioned into a
+regular 3d grid of rectangular bricks, one per processor, based on the
+number of processors in the current simulation and the settings of the
+processors command.  The partitioning can later be
+changed by the balance or fix
+balance commands.
 

 
Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
diff --git a/doc/read_restart.txt b/doc/read_restart.txt
index 7658dd42f6..d08fce975b 100644
--- a/doc/read_restart.txt
+++ b/doc/read_restart.txt
@@ -27,7 +27,15 @@ read_restart poly.*.% :pre
 
 Read in a previously saved simulation from a restart file.  This
 allows continuation of a previous run.  Information about what is
-stored in a restart file is given below.
+stored in a restart file is given below.  Basically this operation
+will re-create the simulation box with all its atoms and their
+attributes, at the point in time it was written to the restart file by
+a previous simluation.  The simulation box will be partitioned into a
+regular 3d grid of rectangular bricks, one per processor, based on the
+number of processors in the current simulation and the settings of the
+"processors"_processors.html command.  The partitioning can later be
+changed by the "balance"_balance.html or "fix
+balance"_fix_balance.html commands.
 
 Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
diff --git a/doc/replicate.html b/doc/replicate.html
index d494e9d225..6b1bac3821 100644
--- a/doc/replicate.html
+++ b/doc/replicate.html
@@ -27,7 +27,12 @@
 For example, replication factors of 2,2,2 will create a simulation
 with 8x as many atoms by doubling the simulation domain in each
 dimension.  A replication factor of 1 in a dimension leaves the
-simulation domain unchanged.
+simulation domain unchanged.  When the new simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the processors command.  The
+partitioning can later be changed by the balance or
+fix balance commands.
 

 
All properties of the atoms are replicated, including their
 velocities, which may or may not be desirable.  New atom IDs are
diff --git a/doc/replicate.txt b/doc/replicate.txt
index 54509e469c..e035bd2821 100644
--- a/doc/replicate.txt
+++ b/doc/replicate.txt
@@ -24,7 +24,12 @@ Replicate the current simulation one or more times in each dimension.
 For example, replication factors of 2,2,2 will create a simulation
 with 8x as many atoms by doubling the simulation domain in each
 dimension.  A replication factor of 1 in a dimension leaves the
-simulation domain unchanged.
+simulation domain unchanged.  When the new simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the "processors"_processors.html command.  The
+partitioning can later be changed by the "balance"_balance.html or
+"fix balance"_fix_balance.html commands.
 
 All properties of the atoms are replicated, including their
 velocities, which may or may not be desirable.  New atom IDs are