See the README.pdf file for more information. diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index 4cccfa734a..a672c23a72 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -205,7 +205,7 @@ The matlab sub-directory contains several "MATLAB"_matlab scripts for post-processing LAMMPS output. The scripts include readers for log and dump files, a reader for EAM potential files, and a converter that reads LAMMPS dump files and produces CFG files that can be visualized -with the "AtomEye"_http://164.107.79.177/Archive/Graphics/A +with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See the README.pdf file for more information. diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html index de94d0293a..065b8c73d3 100644 --- a/doc/pair_dpd.html +++ b/doc/pair_dpd.html @@ -40,13 +40,13 @@ pair_coeff 1 1 1.0 1.0
Style dpd/tstat invokes a DPD thermostat on pairwise interactions, which is equivalent to the non-conservative portion of the DPD force -field. This thermostat can be used in conjunction with any pair -style, and in leiu of per-particle thermostats -like fix langevin or ensemble thermostats like -Nose Hoover as implemented by fix nvt. To use -dpd/stat with another pair style, use the pair_style +field. This thermostat can be used in conjunction with any pair +style, and in leiu of per-particle thermostats like +fix langevin or ensemble thermostats like Nose +Hoover as implemented by fix nvt. To use dpd/stat +with another pair style, use the pair_style hybrid/overlay command to compute both the desired -pair interaction and the thermostat for each pair of particles. +pair interaction and the thermostat for each pair of particles.
For style dpd, the force on atom I due to atom J is given as a sum of 3 terms @@ -148,7 +148,7 @@ atoms.
Related commands:
-pair_coeff, fix nvt, fix
+ pair_coeff, fix nvt, fix
langevin
Default: none
diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt
index 94e325a559..4b2d1081d6 100644
--- a/doc/pair_dpd.txt
+++ b/doc/pair_dpd.txt
@@ -37,12 +37,12 @@ Style {dpd} computes a force field for dissipative particle dynamics
Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
field. This thermostat can be used in conjunction with any "pair
-style"_doc/pair_style.html, and in leiu of per-particle thermostats
-like "fix langevin"_fix_langevin.html or ensemble thermostats like
-Nose Hoover as implemented by "fix nvt"_fix_nvt.html. To use
-{dpd/stat} with another pair style, use the "pair_style
+style"_pair_style.html, and in leiu of per-particle thermostats like
+"fix langevin"_fix_langevin.html or ensemble thermostats like Nose
+Hoover as implemented by "fix nvt"_fix_nh.html. To use {dpd/stat}
+with another pair style, use the "pair_style
hybrid/overlay"_pair_hybrid.html command to compute both the desired
-pair interaction and the thermostat for each pair of particles.
+pair interaction and the thermostat for each pair of particles.
For style {dpd}, the force on atom I due to atom J is given as a sum
of 3 terms
@@ -144,7 +144,7 @@ atoms.
[Related commands:]
-"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nvt.html, "fix
+"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nh.html, "fix
langevin"_fix_langevin.html
[Default:] none
diff --git a/doc/variable.html b/doc/variable.html
index 2983d975b5..f253e530f1 100644
--- a/doc/variable.html
+++ b/doc/variable.html
@@ -76,11 +76,11 @@ which when evaluated produces a single numeric value which can be
output either directly (see the print, fix
print, and run every commands) or as part
of thermodynamic output (see the thermo_style
-command), or used as input to an averaging fix (see the fix
-ave/time command). Variables of style atom store a
-formula which when evaluated produces one numeric value per atom which
-can be output to a dump file (see the dump custom command)
-or used as input to an averaging fix (see the fix
+command), or used as input to an averaging fix (see the fix
+ave/time command). Variables of style atom store
+a formula which when evaluated produces one numeric value per atom
+which can be output to a dump file (see the dump custom
+command) or used as input to an averaging fix (see the fix
ave/spatial and fix ave/atom
commands).
If you want to store the initial volume of the system, you can do it this way: diff --git a/doc/variable.txt b/doc/variable.txt index 5eb2889376..93032f5162 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -71,10 +71,10 @@ output either directly (see the "print"_print.html, "fix print"_fix_print.html, and "run every"_run.html commands) or as part of thermodynamic output (see the "thermo_style"_thermo_style.html command), or used as input to an averaging fix (see the "fix -ave/time"_fix_ave_time command). Variables of style {atom} store a -formula which when evaluated produces one numeric value per atom which -can be output to a dump file (see the "dump custom"_dump.html command) -or used as input to an averaging fix (see the "fix +ave/time"_fix_ave_time.html command). Variables of style {atom} store +a formula which when evaluated produces one numeric value per atom +which can be output to a dump file (see the "dump custom"_dump.html +command) or used as input to an averaging fix (see the "fix ave/spatial"_fix_ave_spatial.html and "fix ave/atom"_fix_ave_atom.html commands). @@ -450,9 +450,9 @@ before a run where the simulation box size changes. You might think this will assign the initial volume to the variable "v". That is not the case. Rather it assigns a formula which evaluates the volume (using the thermo_style keyword "vol") to the variable "v". If you -use the variable "v" in some other command like "fix ave/time" then -the current volume of the box will be evaluated continuously during -the run. +use the variable "v" in some other command like "fix +ave/time"_fix_ave_time.html then the current volume of the box will be +evaluated continuously during the run. If you want to store the initial volume of the system, you can do it this way: