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2015-08-21 22:51:16 +00:00
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doc/doc2/Manual.html.html
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@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="10 Aug 2015 version">
<META NAME="docnumber" CONTENT="19 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>10 Aug 2015 version
<CENTER><H4>19 Aug 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

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doc/doc2/Section_commands.html
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@ -478,7 +478,7 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_smd_contact_radius.html">smd/contact/radius</A></TD><TD ><A HREF = "compute_smd_damage.html">smd/damage</A></TD><TD ><A HREF = "compute_smd_hourglass_error.html">smd/hourglass/error</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_internal_energy.html">smd/internal/energy</A></TD><TD ><A HREF = "compute_smd_plastic_strain.html">smd/plastic/strain</A></TD><TD ><A HREF = "compute_smd_plastic_strain_rate.html">smd/plastic/strain/rate</A></TD><TD ><A HREF = "compute_smd_rho.html">smd/rho</A></TD><TD ><A HREF = "compute_smd_tlsph_defgrad.html">smd/tlsph/defgrad</A></TD><TD ><A HREF = "compute_smd_tlsph_dt.html">smd/tlsph/dt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_tlsph_num_neighs.html">smd/tlsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_tlsph_shape.html">smd/tlsph/shape</A></TD><TD ><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph/strain</A></TD><TD ><A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_tlsph_stress.html">smd/tlsph/stress</A></TD><TD ><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle/mesh/vertices</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain/rate.html">smd/ulsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_ulpsh_stress.html">smd/ulpsh/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain_rate.html">smd/ulsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_ulsph_stress.html">smd/ulsph/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
</TD></TR></TABLE></DIV>

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doc/doc2/Section_example.html
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@ -90,7 +90,7 @@ section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<PRE>cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux < in.indent # run the problem
lmp_linux -in in.indent # run the problem
</PRE>
<P>Running the simulation produces the files <I>dump.indent</I> and
<I>log.lammps</I>. You can visualize the dump file as follows:

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doc/doc2/Section_python.html
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@ -412,7 +412,7 @@ interactively from the bench directory:
on a single processor appear on the screen, the same as if you had
typed something like:
</P>
<PRE>lmp_g++ < in.lj
<PRE>lmp_g++ -in in.lj
</PRE>
<H5><B>Test LAMMPS and Python in parallel:</B>
</H5>
@ -433,7 +433,7 @@ pypar.finalize()
</PRE>
<P>and you should see the same output as if you had typed
</P>
<PRE>% mpirun -np 4 lmp_g++ < in.lj
<PRE>% mpirun -np 4 lmp_g++ -in in.lj
</PRE>
<P>Note that if you leave out the 3 lines from test.py that specify Pypar
commands you will instantiate and run LAMMPS independently on each of

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doc/doc2/Section_start.html
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@ -1213,7 +1213,7 @@ Linux box, using mpirun to launch a parallel job:
make linux
cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux < in.lj
mpirun -np 4 lmp_linux -in in.lj
</PRE>
<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require
@ -1329,8 +1329,8 @@ letter abbreviation can be used:
</UL>
<P>For example, lmp_ibm might be launched as follows:
</P>
<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
</PRE>
<P>Here are the details on the options:
</P>

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doc/doc2/delete_atoms.html
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@ -140,7 +140,7 @@ deletion by the <I>overlap</I> styles. You probably don't want to be
deleting one atom in a bonded pair anyway.
</P>
<P>The <I>bond yes</I> option cannot be used with molecular systems defined
using molecule template files via the <A HREF = "molecular.html">molecule</A> and
using molecule template files via the <A HREF = "molecule.html">molecule</A> and
<A HREF = "atom_style.html">atom_style template</A> commands.
</P>
<P><B>Related commands:</B>

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doc/doc2/package.html
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@ -320,6 +320,13 @@ large cutoffs or with a small number of particles per GPU, increasing
the value can improve performance. The number of threads per atom must
be a power of 2 and currently cannot be greater than 32.
</P>
<P>The <I>blocksize</I> keyword allows to tweak the number of threads used
per thread block. This number should be a multiple of 32 (for GPUs)
and its maximum depends on the specific GPU hardware. Typical choices
are 64, 128, or 256. A larger blocksize increases occupancy of individual
GPU cores, but reduces the total number of thread blocks, thus may lead
to load imbalance.
</P>
<P>The <I>device</I> keyword can be used to tune parameters optimized for a
specific accelerator, when using OpenCL. For CUDA, the <I>device</I>
keyword is ignored. Currently, the device type is limited to NVIDIA

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doc/doc2/pair_lj_cubic.html
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@ -26,16 +26,15 @@ pair_coeff * * 1.0 0.8908987
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/cubic</I> style computes a truncated LJ interaction potential whose
energy and force are continuous everywhere.
Inside the inflection point the interaction is identical to the
standard 12/6 <A HREF = "pair_lj.html">Lennard-Jones</A> potential.
The LJ function outside the inflection point is replaced
with a cubic function of distance. The energy, force, and second
derivative are continuous at the inflection point.
The cubic coefficient A3 is chosen so
that both energy and force go to zero at the cutoff distance.
Outside the cutoff distance the energy and force are zero.
<P>The <I>lj/cubic</I> style computes a truncated LJ interaction potential
whose energy and force are continuous everywhere. Inside the
inflection point the interaction is identical to the standard 12/6
<A HREF = "pair_lj.html">Lennard-Jones</A> potential. The LJ function outside the
inflection point is replaced with a cubic function of distance. The
energy, force, and second derivative are continuous at the inflection
point. The cubic coefficient A3 is chosen so that both energy and
force go to zero at the cutoff distance. Outside the cutoff distance
the energy and force are zero.
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_cubic.jpg">
</CENTER>
@ -47,12 +46,12 @@ the cubic coefficient
A3*rmin^3/epsilon = 27.93... is given in the paper by
Holian and Ravelo <A HREF = "#Holian">(Holian)</A>.
</P>
<P>This potential is commonly used to study the shock mechanics
of FCC solids, as in Ravelo et al. <A HREF = "#Ravelo">(Ravelo)</A>.
<P>This potential is commonly used to study the shock mechanics of FCC
solids, as in Ravelo et al. <A HREF = "#Ravelo">(Ravelo)</A>.
</P>
<P>The following coefficients must be defined for each pair of atom
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example
above, or in the data file or restart files read by the
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
@ -60,9 +59,9 @@ commands, or by mixing as described below:
<LI>sigma (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum, which
is located at rmin = 2^(1/6)*sigma. In the above example, sigma = 0.8908987,
so rmin = 1.
distance for the potential, not as the energy minimum, which is
located at rmin = 2^(1/6)*sigma. In the above example, sigma =
0.8908987, so rmin = 1.
</P>
<HR>