From b7eb7f3301ae9caa7ecb2c5f1a162980e8bf4792 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 22 Jan 2014 18:32:56 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11299 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/dump.html | 42 +++++++++++++++++++++++++++++++++++++++++- doc/dump_modify.html | 9 +++++++++ doc/molecule.html | 19 ++++++++++++++----- doc/molecule.txt | 19 ++++++++++++++----- 4 files changed, 78 insertions(+), 11 deletions(-) diff --git a/doc/dump.html b/doc/dump.html index 36b79b865f..70fd4fe57c 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -25,7 +25,7 @@
  • group-ID = ID of the group of atoms to be dumped -
  • style = atom or cfg or dcd or xtc or xyz or image or molfile or local or custom +
  • style = atom or aotm\mpiio or cfg or dcd or xtc or xyz or xyz/mpiio or image or molfile or local or custom or custom/mpiio
  • N = dump every this many timesteps @@ -34,11 +34,14 @@
  • args = list of arguments for a particular style 
      atom args = none
+  atom/mpiio args = none
   cfg args = same as custom args, see below
   dcd args = none
   xtc args = none
   xyz args = none
    +
      xyz/mpiio args = none 
+
      image args = discussed on dump image doc page 
 
      molfile args = discussed on dump molfile doc page 
@@ -52,6 +55,7 @@
       f_ID[N] = Nth column of local array calculated by a fix with ID 
 
      custom args = list of atom attributes
+  custom/mpiio args = list of atom attributes
     possible attributes = id, mol, type, element, mass,
 			  x, y, z, xs, ys, zs, xu, yu, zu, 
 			  xsu, ysu, zsu, ix, iy, iz,
@@ -96,7 +100,9 @@
 
    Examples:
 
    
 
    dump myDump all atom 100 dump.atom
+dump myDump all atom/mpiio 100 dump.atom.mpiio
 dump 2 subgroup atom 50 dump.run.bin
+dump 2 subgroup atom 50 dump.run.mpiio.bin
 dump 4a all custom 100 dump.myforce.* id type x y vx fx
 dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
 dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
@@ -143,6 +149,15 @@ default.  For the dcd, xtc, xyz, and molfile styles,
 atom ID is on by default. See the dump_modify doc
 page for details.
 
    
+
    As explained below, the atom/mpiio, custom/mpiio, and xyz/mpiio
+styles are identical in command syntax and in the format of the dump
+files they create, to the corresponding styles without "mpiio", except
+the single dump file they produce is written in parallel via the
+MPI-IO library.  For the remainder of this doc page, you should thus
+consider the atom and atom/mpiio styles (etc) to be
+inter-changeable.  The one exception is how the filename is specified
+for the MPI-IO styles, as explained below.
+
    
 
    
 
 
    The style keyword determines what atom quantities are written to the
@@ -352,6 +367,31 @@ when running on large numbers of processors.
 
    Note that using the "*" and "%" characters together can produce a
 large number of small dump files!
 
    
+
    For the atom/mpiio, custom/mpiio, and xyz/mpiio styles, a single
+dump file is written in parallel via the MPI-IO library, which is part
+of the MPI standard for versions 2.0 and above.  Using MPI-IO requires
+two steps.  First, build LAMMPS with its MPIIO package installed, e.g.
+
    
+
    make yes-mpiio    # installs the MPIIO package
+make g++          # build LAMMPS for your platform 
+
    
+
    Second, use a dump filename which contains ".mpiio".  Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO restart files, which must be both written and read using
+MPI-IO, the dump files produced by these MPI-IO styles are identical
+in format to the files produced by their non-MPI-IO style
+counterparts.  This means you can write a dump file using MPI-IO and
+use the read_dump command or perform other
+post-processing, just as if the dump file was not written using
+MPI-IO.
+
    
+
    Note that MPI-IO dump files are one large file which all processors
+write to.  You thus cannot use the "%" wildcard character described
+above in the filename since that specifies generation of multiple
+files.  You can use the ".bin" suffix described below in an MPI-IO
+dump file; again this file will be written in parallel and have the
+same binary format as if it were written without MPI-IO.
+
    
 
    If the filename ends with ".bin", the dump file (or files, if "*" or
 "%" is also used) is written in binary format.  A binary dump file
 will be about the same size as a text version, but will typically
diff --git a/doc/dump_modify.html b/doc/dump_modify.html
index adbf771c4f..19c7f21277 100644
--- a/doc/dump_modify.html
+++ b/doc/dump_modify.html
@@ -121,6 +121,15 @@ dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
 
    Modify the parameters of a previously defined dump command.  Not all
 parameters are relevant to all dump styles.
 
    
+
    As explained on the dump doc page, the atom/mpiio,
+custom/mpiio, and xyz/mpiio dump styles are identical in command
+syntax and in the format of the dump files they create, to the
+corresponding styles without "mpiio", except the single dump file they
+produce is written in parallel via the MPI-IO library.  Thus if a
+dump_modify option below is valid for the atom style, it is also
+valid for the atom/mpiio style, and similarly for the other styles
+which allow for use of MPI-IO.
+
    
 
    
 
 
    
diff --git a/doc/molecule.html b/doc/molecule.html
index 5014f93ab6..888e60b8fc 100644
--- a/doc/molecule.html
+++ b/doc/molecule.html
@@ -13,14 +13,15 @@
 
 
    Syntax:
 
    
-
    molecule ID file 
+
    molecule ID file1 file2 ... 
 
    
 
    • ID = user-assigned name for the molecule template
-
    • file = name of file containing molecule description 
+
    • file1,file2,... = names of files containing molecule descriptions 
 
    
 
    Examples:
 
    
 
    molecule 1 mymol
+molecule 1 co2.txt h2o.txt
 molecule CO2 co2.txt 
 
    
 
    Description:
@@ -35,13 +36,21 @@ templates (or will in the future) include:
 
  • fix rigid/small
 
  • fix shake
 
  • fix gcmc (not yet)
-
  • create_atoms (not yet) 
+
  • create_atoms 
+
  • atom_style template (not yet) 
 
 
    The ID of a molecule template can only contain alphanumeric characters
 and underscores.
 
    
-
    The format of the molecule file is similar to the data file read by
-the read_data commands, and is as follows.
+
    A single template can contain multiple molecules, listed one per file.
+Many of the commands listed above currently use only the first
+molecule in the template, and will issue a warning if the template
+contains multiple molecules.  The atom_style
+template command allows multiple-molecule templates
+to define a system with more than one templated molecule.
+
    
+
    The format of an individual molecule file is similar to the data file
+read by the read_data commands, and is as follows.
 
    
 
    A molecule file has a header and a body.  The header appears first.
 The first line of the header is always skipped; it typically contains
diff --git a/doc/molecule.txt b/doc/molecule.txt
index 6df436200c..2c76cab4fd 100644
--- a/doc/molecule.txt
+++ b/doc/molecule.txt
@@ -10,14 +10,15 @@ molecule command :h3
 
 [Syntax:]
 
-molecule ID file :pre
+molecule ID file1 file2 ... :pre
 
 ID = user-assigned name for the molecule template
-file = name of file containing molecule description :ul
+file1,file2,... = names of files containing molecule descriptions :ul
 
 [Examples:]
 
 molecule 1 mymol
+molecule 1 co2.txt h2o.txt
 molecule CO2 co2.txt :pre
 
 [Description:]
@@ -32,13 +33,21 @@ templates (or will in the future) include:
 "fix rigid/small"_fix_rigid.html
 "fix shake"_fix_shake.html
 "fix gcmc"_fix_gcmc.html (not yet)
-"create_atoms"_create_atoms.html (not yet) :ul
+"create_atoms"_create_atoms.html 
+"atom_style template"_atom_style.html (not yet) :ul
 
 The ID of a molecule template can only contain alphanumeric characters
 and underscores.
 
-The format of the molecule file is similar to the data file read by
-the "read_data"_read_data.html commands, and is as follows.
+A single template can contain multiple molecules, listed one per file.
+Many of the commands listed above currently use only the first
+molecule in the template, and will issue a warning if the template
+contains multiple molecules.  The "atom_style
+template"_atom_style.html command allows multiple-molecule templates
+to define a system with more than one templated molecule.
+
+The format of an individual molecule file is similar to the data file
+read by the "read_data"_read_data.html commands, and is as follows.
 
 A molecule file has a header and a body.  The header appears first.
 The first line of the header is always skipped; it typically contains