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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13929 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-08-21 22:51:16 +00:00
parent 717ecf0a09
commit f5388bbbb2
8 changed files with 34 additions and 28 deletions
--- a/doc/doc2/Manual.html.html
+++ b/doc/doc2/Manual.html.html
@ -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>
--- a/doc/doc2/Section_commands.html
+++ b/doc/doc2/Section_commands.html
@ -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>
--- a/doc/doc2/Section_example.html
+++ b/doc/doc2/Section_example.html
@ -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:
--- a/doc/doc2/Section_python.html
+++ b/doc/doc2/Section_python.html
@ -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
--- a/doc/doc2/Section_start.html
+++ b/doc/doc2/Section_start.html
@ -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
+<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.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>
--- a/doc/doc2/delete_atoms.html
+++ b/doc/doc2/delete_atoms.html
@ -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>
--- a/doc/doc2/package.html
+++ b/doc/doc2/package.html
@ -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
--- a/doc/doc2/pair_lj_cubic.html
+++ b/doc/doc2/pair_lj_cubic.html
@ -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
+<P>The <I>lj/cubic</I> style computes a truncated LJ interaction potential
-energy and force are continuous everywhere. 
+whose energy and force are continuous everywhere.  Inside the
-Inside the inflection point the interaction is identical to the 
+inflection point the interaction is identical to the standard 12/6
-standard 12/6 <A HREF = "pair_lj.html">Lennard-Jones</A> potential.
+<A HREF = "pair_lj.html">Lennard-Jones</A> potential.  The LJ function outside the
-The LJ function outside the inflection point is replaced 
+inflection point is replaced with a cubic function of distance. The
-with a cubic function of distance. The energy, force, and second
+energy, force, and second derivative are continuous at the inflection
-derivative are continuous at the inflection point. 
+point.  The cubic coefficient A3 is chosen so that both energy and
-The cubic coefficient A3 is chosen so
+force go to zero at the cutoff distance.  Outside the cutoff distance
-that both energy and force go to zero at the cutoff distance. 
+the energy and force are zero.
 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
+<P>This potential is commonly used to study the shock mechanics of FCC
-of FCC solids, as in Ravelo et al. <A HREF = "#Ravelo">(Ravelo)</A>.
+solids, as in Ravelo et al. <A HREF = "#Ravelo">(Ravelo)</A>.
 </P>
-<P>The following coefficients must be defined for each pair of atom
+<P>The following coefficients must be defined for each pair of atom types
-types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example above,
-above, or in the data file or restart files read by the
+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
+distance for the potential, not as the energy minimum, which is
-is located at rmin = 2^(1/6)*sigma. In the above example, sigma = 0.8908987,
+located at rmin = 2^(1/6)*sigma. In the above example, sigma =
-so rmin = 1.
+0.8908987, so rmin = 1.
 </P>
 <HR>