From 06f25e66082f8eb178fee5e02914ec484e538271 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 19 Aug 2015 15:38:23 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13911 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_commands.html | 26 +++---- doc/doc2/Section_start.html | 13 +++- doc/doc2/dump.html | 39 ++++++++-- doc/doc2/dump_h5md.html | 136 +++++++++++++++++++++++++++++++++ doc/doc2/package.html | 2 + doc/doc2/pair_lj_cubic.html | 2 + doc/doc2/pair_tersoff.html | 4 +- doc/doc2/pair_zbl.html | 2 + 8 files changed, 203 insertions(+), 21 deletions(-) create mode 100644 doc/doc2/dump_h5md.html diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index 427f4b8253..bb0a097c9b 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -509,19 +509,19 @@ KOKKOS, o = USER-OMP, t = OPT. hbond/dreiding/lj (o)hbond/dreiding/morse (o)kimlcbop line/lj (o)lj/charmm/coul/charmm (cko)lj/charmm/coul/charmm/implicit (cko)lj/charmm/coul/long (cgiko) lj/charmm/coul/msmlj/class2 (cgko)lj/class2/coul/cut (cko)lj/class2/coul/long (cgko) -lj/cut (cgikot)lj/cut/coul/cut (cgko)lj/cut/coul/debye (cgko)lj/cut/coul/dsf (gko) -lj/cut/coul/long (cgikot)lj/cut/coul/msm (go)lj/cut/dipole/cut (go)lj/cut/dipole/long -lj/cut/tip4p/cut (o)lj/cut/tip4p/long (ot)lj/expand (cgko)lj/gromacs (cgko) -lj/gromacs/coul/gromacs (cko)lj/long/coul/long (o)lj/long/dipole/longlj/long/tip4p/long -lj/smooth (co)lj/smooth/linear (o)lj96/cut (cgo)lubricate (o) -lubricate/poly (o)lubricateUlubricateU/polymeam (o) -mie/cut (o)morse (cgot)nb3b/harmonic (o)nm/cut (o) -nm/cut/coul/cut (o)nm/cut/coul/long (o)peri/epsperi/lps (o) -peri/pmb (o)peri/vespolymorphicreax -rebo (o)resquared (go)snapsoft (go) -sw (cgkio)table (gko)tersoff (cko)tersoff/mod (ko) -tersoff/zbl (ko)tip4p/cut (o)tip4p/long (o)tri/lj (o) -yukawa (go)yukawa/colloid (go)zbl (o) +lj/cubic (go)lj/cut (cgikot)lj/cut/coul/cut (cgko)lj/cut/coul/debye (cgko) +lj/cut/coul/dsf (gko)lj/cut/coul/long (cgikot)lj/cut/coul/msm (go)lj/cut/dipole/cut (go) +lj/cut/dipole/longlj/cut/tip4p/cut (o)lj/cut/tip4p/long (ot)lj/expand (cgko) +lj/gromacs (cgko)lj/gromacs/coul/gromacs (cko)lj/long/coul/long (o)lj/long/dipole/long +lj/long/tip4p/longlj/smooth (co)lj/smooth/linear (o)lj96/cut (cgo) +lubricate (o)lubricate/poly (o)lubricateUlubricateU/poly +meam (o)mie/cut (o)morse (cgot)nb3b/harmonic (o) +nm/cut (o)nm/cut/coul/cut (o)nm/cut/coul/long (o)peri/eps +peri/lps (o)peri/pmb (o)peri/vespolymorphic +reaxrebo (o)resquared (go)snap +soft (go)sw (cgkio)table (gko)tersoff (cgko) +tersoff/mod (ko)tersoff/zbl (ko)tip4p/cut (o)tip4p/long (o) +tri/lj (o)yukawa (go)yukawa/colloid (go)zbl (go)

These are additional pair styles in USER packages, which can be used diff --git a/doc/doc2/Section_start.html b/doc/doc2/Section_start.html index bf0da87989..acc1beac4d 100644 --- a/doc/doc2/Section_start.html +++ b/doc/doc2/Section_start.html @@ -272,9 +272,17 @@ within the LAMMPS code. The options that are currently recogized are:

The read_data and dump commands will read/write gzipped files if you compile with -DLAMMPS_GZIP. It requires that your machine supports -the "popen" function in the standard runtime library and that a gzip +the "popen()" function in the standard runtime library and that a gzip executable can be found by LAMMPS during a run.

+

IMPORTANT NOTE: on some clusters with high-speed networks, using the +fork() library calls (required by popen()) can interfere with the fast +communication library and lead to simulations using compressed output +or input to hang or crash. For selected operations, compressed file +I/O is also available using a compression library instead, which are +provided in the COMPRESS package. From more details about compiling +LAMMPS with packages, please see below. +

If you use -DLAMMPS_JPEG, the dump image command will be able to write out JPEG image files. For JPEG files, you must also link LAMMPS with a JPEG library, as described below. If you use @@ -290,6 +298,9 @@ the need to store intermediate image files. It requires that your machines supports the "popen" function in the standard runtime library and that an FFmpeg executable can be found by LAMMPS during the run.

+

IMPORTANT NOTE: Similar to the note above, this option can conflict +with high-speed networks, because it uses popen(). +

Using -DLAMMPS_MEMALIGN= enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. This can help to make more efficient use of diff --git a/doc/doc2/dump.html b/doc/doc2/dump.html index 05256568a7..08d97ed84a 100644 --- a/doc/doc2/dump.html +++ b/doc/doc2/dump.html @@ -11,6 +11,8 @@

dump command

+

dump h5md command +

dump image command

dump movie command @@ -25,7 +27,7 @@
  • group-ID = ID of the group of atoms to be dumped -
  • style = atom or atom/mpiio or cfg or cfg/mpiio or dcd or xtc or xyz or xyz/mpiio or image or movie or molfile or local or custom or custom/mpiio +
  • style = atom or atom/gz or atom/mpiio or cfg or cfg/gz or cfg/mpiio or dcd or xtc or xyz or xyz/gz or xyz/mpiio or h5md or image or movie or molfile or local or custom or custom/gz or custom/mpiio
  • N = dump every this many timesteps @@ -34,15 +36,21 @@
  • args = list of arguments for a particular style 
      atom args = none
+  atom/gz args = none
   atom/mpiio args = none
   cfg args = same as custom args, see below
+  cfg/gz args = same as custom args, see below
   cfg/mpiio args = same as custom args, see below
   dcd args = none
   xtc args = none
   xyz args = none
    +
      xyz/gz args = none 
+
      xyz/mpiio args = none
    +
      h5md args = discussed on dump h5md doc page 
+
      image args = discussed on dump image doc page 
 
      movie args = discussed on dump image doc page 
@@ -57,7 +65,7 @@
       f_ID = local vector calculated by a fix with ID
       f_ID[N] = Nth column of local array calculated by a fix with ID
    -
      custom or custom/mpiio args = list of atom attributes
+
      custom or custom/gz or custom/mpiio args = list of atom attributes
     possible attributes = id, mol, proc, procp1, type, element, mass,
 			  x, y, z, xs, ys, zs, xu, yu, zu, 
 			  xsu, ysu, zsu, ix, iy, iz,
@@ -102,6 +110,7 @@
 
    
 
    dump myDump all atom 100 dump.atom
 dump myDump all atom/mpiio 100 dump.atom.mpiio
+dump myDump all atom/gz 100 dump.atom.gz
 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
@@ -150,6 +159,17 @@ default.  For the dcd, xtc, xyz, and molfile styles,
 atom ID is on by default. See the dump_modify doc
 page for details.
 
    
+
    The atom/gz, cfg/gz, custom/gz, and xyz/gz styles are identical
+in command syntax to the corresponding styles without "gz", however,
+they generate compressed files using the zlib library. Thus the filename
+suffix ".gz" is mandatory. This is an alternative approach to writing
+compressed files via a pipe, as done by the regular dump styles, which
+may be required on clusters where the interface to the high-speed network
+disallows using the fork() library call (which is needed for a pipe).
+For the remainder of this doc page, you should thus consider the atom
+and atom/gz styles (etc) to be inter-changeable, with the exception
+of the required filename suffix.
+
    
 
    As explained below, the atom/mpiio, cfg/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
@@ -583,9 +603,15 @@ per-atom quantities which could then be output into dump files.
 
 
    Restrictions:
 
    
-
    To write gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the Making
-LAMMPS section of the documentation.
+
    To write gzipped dump files, you must either compile LAMMPS with the
+-DLAMMPS_GZIP option or use the styles from the COMPRESS package
+- see the Making LAMMPS section of
+the documentation.
+
    
+
    The atom/gz, cfg/gz, custom/gz, and xyz/gz styles are part
+of the COMPRESS package.  They are only enabled if LAMMPS was built
+with that package.  See the Making
+LAMMPS section for more info.
 
    
 
    The atom/mpiio, cfg/mpiio, custom/mpiio, and xyz/mpiio styles
 are part of the MPIIO package.  They are only enabled if LAMMPS was
@@ -611,7 +637,8 @@ machines.
 
    
 
    Related commands:
 
    
-
    dump image, dump_modify,
+
    dump h5md, dump image,
+dump molfile, dump_modify,
 undump
 
    
 
    Default:
diff --git a/doc/doc2/dump_h5md.html b/doc/doc2/dump_h5md.html
new file mode 100644
index 0000000000..0c6db43234
--- /dev/null
+++ b/doc/doc2/dump_h5md.html
@@ -0,0 +1,136 @@
+
+
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
+
    
+
+
+
+
+
+
+
    
+
+
    dump h5md command 
+
    
+
    Syntax:
+
    
+
    dump ID group-ID h5md N file.h5 args 
+
    
+
    • ID = user-assigned name for the dump 
+
+
    • group-ID = ID of the group of atoms to be imaged 
+
+
    • h5md = style of dump command (other styles atom or cfg or dcd or xtc or xyz or local or custom are discussed on the dump doc page) 
+
+
    • N = dump every this many timesteps 
+
+
    • file.h5 = name of file to write to 
+
+
    • args = list of data elements to dump, with their dump "subintervals".
+At least one element must be given and image may only be present if
+position is specified first. 
+
+
        position options
+  image
+  velocity options
+  force options
+  species options
+  file_from ID: do not open a new file, re-use the already opened file from dump ID
+  box value = yes or no
+  create_group value = yes or no
+  author value = quoted string 
+
      
+
      For the elements position, velocity, force and species, one
+may specify a sub-interval to write the data only every N_element
+iterations of the dump (i.e. every N*N_element time steps). This is
+specified by the option
+
      
+
        every N_element 
+
      
+
      that follows directly the element declaration.
+
      
+
+
    
+
    Examples:
+
    
+
    dump h5md1 all h5md 100 dump_h5md.h5 position image
+dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
+dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" 
+
    
+
    Description:
+
    
+
    Dump a snapshot of atom coordinates every N timesteps in the
+HDF5 based H5MD file format (de Buyl).
+HDF5 files are binary, portable and self-describing.  This dump style
+will write only one file, on the root node.
+
    
+
    Several dumps may write to the same file, by using file_from and
+referring to a previously defined dump.  Several groups may also be
+stored within the same file by defining several dumps.  A dump that
+refers (via file_from) to an already open dump ID and that concerns
+another particle group must specify create_group yes.
+
    
+
+
+
    Each data element is written every N*N_element steps. For image, no
+subinterval is needed as it must be present at the same interval as
+position.  image must be given after position in any case.  The
+box information (edges in each dimension) is stored at the same
+interval than the position element, if present. Else it is stored
+every N steps.
+
    
+
    IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.
+
    
+
    Use from write_dump:
+
    
+
    It is possible to use this dump style with the
+write_dump command.  In this case, the subintervals
+must not be set at all.  The write_dump command can be used either to
+create a new file or to add current data to an existing dump file by
+using the file_from keyword.
+
    
+
    Typically, the species data is fixed. The following two commands
+store the position data every 100 timesteps, with the image data, and
+store once the species data in the same file.
+
    
+
    dump h5md1 all h5md 100 dump.h5 position image
+write_dump all h5md dump.h5 file_from h5md1 species 
+
    
+
    
+
+
    Restrictions:
+
    
+
    The number of atoms per snapshot cannot change with the h5md style.
+The position data is stored wrapped (box boundaries not enforced, see
+note above).  Only orthogonal domains are currently supported. This is
+a limitation of the present dump h5md command and not of H5MD itself.
+
    
+
    The h5md dump style is part of the USER-H5MD package. It is only
+enabled if LAMMPS was built with that package. See the Making
+LAMMPS section for more info. It also
+requires (i) building the ch5md library provided with LAMMPS (See the
+Making LAMMPS section for more info.) and
+(ii) having the HDF5 library installed (C bindings are
+sufficient) on your system.  The library ch5md is compiled with the
+h5cc wrapper provided by the HDF5 library.
+
    
+
+
+
    
+
+
    Related commands:
+
    
+
    dump, dump_modify, undump
+
    
+
    
+
+
+
+
    (de Buyl) de Buyl, Colberg and Hofling, H5MD: A structured,
+efficient, and portable file format for molecular data,
+Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
+[arXiv:1308.6382].
+
    
+
diff --git a/doc/doc2/package.html b/doc/doc2/package.html
index 5c0dd866d8..d4b2a4fa52 100644
--- a/doc/doc2/package.html
+++ b/doc/doc2/package.html
@@ -56,6 +56,8 @@
         Nthreads = # of GPU threads used per atom
       device value = device_type
         device_type = kepler or fermi or cypress or generic
+      blocksize value = size
+        size = thread block size for pair force computation
   intel args = NPhi keyword value ...
     Nphi = # of coprocessors per node
     zero or more keyword/value pairs may be appended 
diff --git a/doc/doc2/pair_lj_cubic.html b/doc/doc2/pair_lj_cubic.html
index 386a41988e..e173da74a1 100644
--- a/doc/doc2/pair_lj_cubic.html
+++ b/doc/doc2/pair_lj_cubic.html
@@ -11,6 +11,8 @@
 
 
    pair_style lj/cubic command 
 
    
+
    pair_style lj/cubic/gpu command 
+
    
 
    pair_style lj/cubic/omp command 
 
    
 
    Syntax:
diff --git a/doc/doc2/pair_tersoff.html b/doc/doc2/pair_tersoff.html
index 1d17fc697e..4e4540c87e 100644
--- a/doc/doc2/pair_tersoff.html
+++ b/doc/doc2/pair_tersoff.html
@@ -15,6 +15,8 @@

    • pair_style tersoff/cuda

    +

    pair_style tersoff/gpu +

    pair_style tersoff/kk

    pair_style tersoff/omp @@ -25,7 +27,7 @@ 

    pair_style style
    -

    style = tersoff or tersoff/table or tersoff/cuda or tersoff/omp or tersoff/table/omp +

    style = tersoff or tersoff/table or tersoff/cuda or tersoff/gpu or tersoff/omp or tersoff/table/omp

    Examples:

    diff --git a/doc/doc2/pair_zbl.html b/doc/doc2/pair_zbl.html index ad0b945578..6bc9e2cf1a 100644 --- a/doc/doc2/pair_zbl.html +++ b/doc/doc2/pair_zbl.html @@ -11,6 +11,8 @@

    pair_style zbl command

    +

    pair_style zbl/gpu command +

    pair_style zbl/omp command

    Syntax: