forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13911 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
cd861535f0
commit
06f25e6608
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@ -509,19 +509,19 @@ KOKKOS, o = USER-OMP, t = OPT.
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<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgiko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (cko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (cko)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (o)</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_cubic.html">lj/cubic (go)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (cgko)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (go)</A>
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</TD></TR></TABLE></DIV>
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<P>These are additional pair styles in USER packages, which can be used
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@ -272,9 +272,17 @@ within the LAMMPS code. The options that are currently recogized are:
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</UL>
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<P>The read_data and dump commands will read/write gzipped files if you
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compile with -DLAMMPS_GZIP. It requires that your machine supports
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the "popen" function in the standard runtime library and that a gzip
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the "popen()" function in the standard runtime library and that a gzip
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executable can be found by LAMMPS during a run.
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</P>
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<P>IMPORTANT NOTE: on some clusters with high-speed networks, using the
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fork() library calls (required by popen()) can interfere with the fast
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communication library and lead to simulations using compressed output
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or input to hang or crash. For selected operations, compressed file
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I/O is also available using a compression library instead, which are
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provided in the COMPRESS package. From more details about compiling
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LAMMPS with packages, please see below.
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</P>
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<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump_image.html">dump image</A> command
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will be able to write out JPEG image files. For JPEG files, you must
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also link LAMMPS with a JPEG library, as described below. If you use
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@ -290,6 +298,9 @@ the need to store intermediate image files. It requires that your
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machines supports the "popen" function in the standard runtime library
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and that an FFmpeg executable can be found by LAMMPS during the run.
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</P>
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<P>IMPORTANT NOTE: Similar to the note above, this option can conflict
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with high-speed networks, because it uses popen().
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</P>
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<P>Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
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posix_memalign() call instead of malloc() when large chunks or memory
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are allocated by LAMMPS. This can help to make more efficient use of
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@ -11,6 +11,8 @@
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<H3>dump command
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</H3>
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<H3><A HREF = "dump_h5md.html">dump h5md</A> command
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</H3>
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<H3><A HREF = "dump_image.html">dump image</A> command
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</H3>
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<H3><A HREF = "dump_image.html">dump movie</A> command
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@ -25,7 +27,7 @@
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<LI>group-ID = ID of the group of atoms to be dumped
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<LI>style = <I>atom</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>cfg/mpiio</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>movie</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
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<LI>style = <I>atom</I> or <I>atom/gz</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>cfg/gz</I> or <I>cfg/mpiio</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/gz</I> or <I>xyz/mpiio</I> or <I>h5md</I> or <I>image</I> or <I>movie</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/gz</I> or <I>custom/mpiio</I>
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<LI>N = dump every this many timesteps
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@ -34,15 +36,21 @@
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<LI>args = list of arguments for a particular style
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<PRE> <I>atom</I> args = none
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<I>atom/gz</I> args = none
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<I>atom/mpiio</I> args = none
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<I>cfg</I> args = same as <I>custom</I> args, see below
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<I>cfg/gz</I> args = same as <I>custom</I> args, see below
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<I>cfg/mpiio</I> args = same as <I>custom</I> args, see below
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<I>dcd</I> args = none
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<I>xtc</I> args = none
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<I>xyz</I> args = none
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</PRE>
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<PRE> <I>xyz/gz</I> args = none
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</PRE>
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<PRE> <I>xyz/mpiio</I> args = none
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</PRE>
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<PRE> <I>h5md</I> args = discussed on <A HREF = "dump_h5md.html">dump h5md</A> doc page
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</PRE>
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<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
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</PRE>
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<PRE> <I>movie</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
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@ -57,7 +65,7 @@
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f_ID = local vector calculated by a fix with ID
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f_ID[N] = Nth column of local array calculated by a fix with ID
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</PRE>
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<PRE> <I>custom</I> or <I>custom/mpiio</I> args = list of atom attributes
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<PRE> <I>custom</I> or <I>custom/gz</I> or <I>custom/mpiio</I> args = list of atom attributes
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possible attributes = id, mol, proc, procp1, type, element, mass,
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x, y, z, xs, ys, zs, xu, yu, zu,
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xsu, ysu, zsu, ix, iy, iz,
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@ -102,6 +110,7 @@
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</P>
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<PRE>dump myDump all atom 100 dump.atom
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dump myDump all atom/mpiio 100 dump.atom.mpiio
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dump myDump all atom/gz 100 dump.atom.gz
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dump 2 subgroup atom 50 dump.run.bin
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dump 2 subgroup atom 50 dump.run.mpiio.bin
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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@ -150,6 +159,17 @@ default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles,
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atom ID is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc
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page for details.
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</P>
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<P>The <I>atom/gz</I>, <I>cfg/gz</I>, <I>custom/gz</I>, and <I>xyz/gz</I> styles are identical
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in command syntax to the corresponding styles without "gz", however,
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they generate compressed files using the zlib library. Thus the filename
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suffix ".gz" is mandatory. This is an alternative approach to writing
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compressed files via a pipe, as done by the regular dump styles, which
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may be required on clusters where the interface to the high-speed network
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disallows using the fork() library call (which is needed for a pipe).
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For the remainder of this doc page, you should thus consider the <I>atom</I>
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and <I>atom/gz</I> styles (etc) to be inter-changeable, with the exception
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of the required filename suffix.
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</P>
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<P>As explained below, the <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and
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<I>xyz/mpiio</I> styles are identical in command syntax and in the format
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of the dump files they create, to the corresponding styles without
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@ -583,9 +603,15 @@ per-atom quantities which could then be output into dump files.
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<P><B>Restrictions:</B>
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</P>
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<P>To write gzipped dump files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
|
||||
LAMMPS</A> section of the documentation.
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<P>To write gzipped dump files, you must either compile LAMMPS with the
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-DLAMMPS_GZIP option or use the styles from the COMPRESS package
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- see the <A HREF = "Section_start.html#start_2">Making LAMMPS</A> section of
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the documentation.
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</P>
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||||
<P>The <I>atom/gz</I>, <I>cfg/gz</I>, <I>custom/gz</I>, and <I>xyz/gz</I> styles are part
|
||||
of the COMPRESS package. They are only enabled if LAMMPS was built
|
||||
with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>The <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles
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are part of the MPIIO package. They are only enabled if LAMMPS was
|
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|
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@ -611,7 +637,8 @@ machines.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "dump_image.html">dump image</A>, <A HREF = "dump_modify.html">dump_modify</A>,
|
||||
<P><A HREF = "dump_h5md.html">dump h5md</A>, <A HREF = "dump_image.html">dump image</A>,
|
||||
<A HREF = "dump_molfile.html">dump molfile</A>, <A HREF = "dump_modify.html">dump_modify</A>,
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||||
<A HREF = "undump.html">undump</A>
|
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</P>
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<P><B>Default:</B>
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||||
|
|
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|
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@ -0,0 +1,136 @@
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<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
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<HR>
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||||
|
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<H3>dump h5md command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>dump ID group-ID h5md N file.h5 args
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</PRE>
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<UL><LI>ID = user-assigned name for the dump
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||||
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<LI>group-ID = ID of the group of atoms to be imaged
|
||||
|
||||
<LI>h5md = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
|
||||
|
||||
<LI>N = dump every this many timesteps
|
||||
|
||||
<LI>file.h5 = name of file to write to
|
||||
|
||||
<LI>args = list of data elements to dump, with their dump "subintervals".
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||||
At least one element must be given and image may only be present if
|
||||
position is specified first.
|
||||
|
||||
<PRE> 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 = <I>yes</I> or <I>no</I>
|
||||
create_group value = <I>yes</I> or <I>no</I>
|
||||
author value = quoted string
|
||||
</PRE>
|
||||
<P>For the elements <I>position</I>, <I>velocity</I>, <I>force</I> and <I>species</I>, 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
|
||||
</P>
|
||||
<PRE> every N_element
|
||||
</PRE>
|
||||
<P>that follows directly the element declaration.
|
||||
</P>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>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"
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Dump a snapshot of atom coordinates every N timesteps in the
|
||||
<A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A> based <A HREF = "http://nongnu.org/h5md/">H5MD</A> file format <A HREF = "#h5md_cpc">(de Buyl)</A>.
|
||||
HDF5 files are binary, portable and self-describing. This dump style
|
||||
will write only one file, on the root node.
|
||||
</P>
|
||||
<P>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 <I>file_from</I>) to an already open dump ID and that concerns
|
||||
another particle group must specify <I>create_group yes</I>.
|
||||
</P>
|
||||
|
||||
|
||||
<P>Each data element is written every N*N_element steps. For <I>image</I>, no
|
||||
subinterval is needed as it must be present at the same interval as
|
||||
<I>position</I>. <I>image</I> must be given after <I>position</I> in any case. The
|
||||
box information (edges in each dimension) is stored at the same
|
||||
interval than the <I>position</I> element, if present. Else it is stored
|
||||
every N steps.
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<P><B>Use from write_dump:</B>
|
||||
</P>
|
||||
<P>It is possible to use this dump style with the
|
||||
<A HREF = "write_dump.html">write_dump</A> 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 <I>file_from</I> keyword.
|
||||
</P>
|
||||
<P>Typically, the <I>species</I> 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.
|
||||
</P>
|
||||
<PRE>dump h5md1 all h5md 100 dump.h5 position image
|
||||
write_dump all h5md dump.h5 file_from h5md1 species
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>The <I>h5md</I> dump style is part of the USER-H5MD package. It is only
|
||||
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info. It also
|
||||
requires (i) building the ch5md library provided with LAMMPS (See the
|
||||
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.) and
|
||||
(ii) having the <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A> library installed (C bindings are
|
||||
sufficient) on your system. The library ch5md is compiled with the
|
||||
h5cc wrapper provided by the HDF5 library.
|
||||
</P>
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "h5md_cpc"></A>
|
||||
|
||||
<P><B>(de Buyl)</B> de Buyl, Colberg and Hofling, H5MD: A structured,
|
||||
efficient, and portable file format for molecular data,
|
||||
Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
|
||||
<A HREF = "http://arxiv.org/abs/1308.6382/">[arXiv:1308.6382]</A>.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -56,6 +56,8 @@
|
|||
Nthreads = # of GPU threads used per atom
|
||||
<I>device</I> value = device_type
|
||||
device_type = <I>kepler</I> or <I>fermi</I> or <I>cypress</I> or <I>generic</I>
|
||||
<I>blocksize</I> value = size
|
||||
size = thread block size for pair force computation
|
||||
<I>intel</I> args = NPhi keyword value ...
|
||||
Nphi = # of coprocessors per node
|
||||
zero or more keyword/value pairs may be appended
|
||||
|
|
|
|||
|
|
@ -11,6 +11,8 @@
|
|||
|
||||
<H3>pair_style lj/cubic command
|
||||
</H3>
|
||||
<H3>pair_style lj/cubic/gpu command
|
||||
</H3>
|
||||
<H3>pair_style lj/cubic/omp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
|
|
|
|||
|
|
@ -15,6 +15,8 @@
|
|||
</H3>
|
||||
<H3>pair_style tersoff/cuda
|
||||
</H3>
|
||||
<H3>pair_style tersoff/gpu
|
||||
</H3>
|
||||
<H3>pair_style tersoff/kk
|
||||
</H3>
|
||||
<H3>pair_style tersoff/omp
|
||||
|
|
@ -25,7 +27,7 @@
|
|||
</P>
|
||||
<PRE>pair_style style
|
||||
</PRE>
|
||||
<P>style = <I>tersoff</I> or <I>tersoff/table</I> or <I>tersoff/cuda</I> or <I>tersoff/omp</I> or <I>tersoff/table/omp</I>
|
||||
<P>style = <I>tersoff</I> or <I>tersoff/table</I> or <I>tersoff/cuda</I> or <I>tersoff/gpu</I> or <I>tersoff/omp</I> or <I>tersoff/table/omp</I>
|
||||
</P>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -11,6 +11,8 @@
|
|||
|
||||
<H3>pair_style zbl command
|
||||
</H3>
|
||||
<H3>pair_style zbl/gpu command
|
||||
</H3>
|
||||
<H3>pair_style zbl/omp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
|
|
|
|||
Loading…
Reference in New Issue