git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7326 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_accelerate.html

@@ -11,8 +11,18 @@ Section</A>
 
 <HR>
 
-<H3>5. Using accelerated CPU and GPU styles 
+<H3>5. Accelerating LAMMPS performance 
 </H3>
+<P>This section describes various methods for improving LAMMPS
+performance for different classes of problems running
+on different kinds of machines.
+</P>
+5.1 <A HREF = "#acc_1">OPT package</A><BR>
+5.2 <A HREF = "#acc_2">USER-OMP package</A><BR>
+5.3 <A HREF = "#acc_3">GPU package</A><BR>
+5.4 <A HREF = "#acc_4">USER-CUDA package</A><BR>
+5.5 <A HREF = "#acc_5">Comparison of GPU and USER-CUDA packages</A> <BR>
+
 <P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
 <A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
 been added to LAMMPS, which will typically run faster than the
@@ -74,12 +84,6 @@ compute, and kspace sections.
 <P>The final section compares and contrasts the GPU and USER-CUDA
 packages, since they are both designed to use NVIDIA GPU hardware.
 </P>
-5.1 <A HREF = "#acc_1">OPT package</A><BR>
-5.2 <A HREF = "#acc_2">USER-OMP package</A><BR>
-5.3 <A HREF = "#acc_3">GPU package</A><BR>
-5.4 <A HREF = "#acc_4">USER-CUDA package</A><BR>
-5.5 <A HREF = "#acc_5">Comparison of GPU and USER-CUDA packages</A> <BR>
-
 <HR>
 
 <HR>

doc/Section_accelerate.txt

@@ -8,7 +8,17 @@ Section"_Section_howto.html :c
 
 :line
 
-5. Using accelerated CPU and GPU styles :h3
+5. Accelerating LAMMPS performance :h3
+
+This section describes various methods for improving LAMMPS
+performance for different classes of problems running
+on different kinds of machines.
+
+5.1 "OPT package"_#acc_1
+5.2 "USER-OMP package"_#acc_2
+5.3 "GPU package"_#acc_3
+5.4 "USER-CUDA package"_#acc_4
+5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b)
 
 Accelerated versions of various "pair_style"_pair_style.html,
 "fixes"_fix.html, "computes"_compute.html, and other commands have
@@ -71,12 +81,6 @@ speed-ups you can expect :ul
 The final section compares and contrasts the GPU and USER-CUDA
 packages, since they are both designed to use NVIDIA GPU hardware.
 
-5.1 "OPT package"_#acc_1
-5.2 "USER-OMP package"_#acc_2
-5.3 "GPU package"_#acc_3
-5.4 "USER-CUDA package"_#acc_4
-5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b)
-
 :line
 :line
 

doc/Section_commands.html

@@ -11,8 +11,8 @@
 
 <H3>3. Commands 
 </H3>
-<P>This section describes how a LAMMPS input script is formatted and what
+<P>This section describes how a LAMMPS input script is formatted and the
-commands are used to define a LAMMPS simulation.
+input script commands used to define a LAMMPS simulation.
 </P>
 3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
 3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
@@ -22,6 +22,8 @@ commands are used to define a LAMMPS simulation.
 
 <HR>
 
+<HR>
+
 <A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script 
 </H4>
 <P>LAMMPS executes by reading commands from a input script (text file),

doc/Section_commands.txt

@@ -8,8 +8,8 @@
 
 3. Commands :h3
 
-This section describes how a LAMMPS input script is formatted and what
+This section describes how a LAMMPS input script is formatted and the
-commands are used to define a LAMMPS simulation.
+input script commands used to define a LAMMPS simulation.
 
 3.1 "LAMMPS input script"_#cmd_1
 3.2 "Parsing rules"_#cmd_2
@@ -17,6 +17,7 @@ commands are used to define a LAMMPS simulation.
 3.4 "Commands listed by category"_#cmd_4
 3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
 
+:line
 :line
 
 3.1 LAMMPS input script :link(cmd_1),h4

doc/Section_errors.html

@@ -13,8 +13,8 @@ Section</A>
 
 <H3>12. Errors 
 </H3>
-<P>This section describes the various kinds of errors you can encounter
+<P>This section describes the errors you can encounter when using LAMMPS,
-when using LAMMPS.
+either conceptually, or as printed out by the program.
 </P>
 12.1 <A HREF = "#err_1">Common problems</A><BR>
 12.2 <A HREF = "#err_2">Reporting bugs</A><BR>
@@ -22,6 +22,8 @@ when using LAMMPS.
 
 <HR>
 
+<HR>
+
 <A NAME = "err_1"></A><H4>12.1 Common problems 
 </H4>
 <P>If two LAMMPS runs do not produce the same answer on different

doc/Section_errors.txt

@@ -10,13 +10,14 @@ Section"_Section_history.html :c
 
 12. Errors :h3
 
-This section describes the various kinds of errors you can encounter
+This section describes the errors you can encounter when using LAMMPS,
-when using LAMMPS.
+either conceptually, or as printed out by the program.
 
 12.1 "Common problems"_#err_1
 12.2 "Reporting bugs"_#err_2
 12.3 "Error & warning messages"_#err_3 :all(b)
 
+:line
 :line
 
 12.1 Common problems :link(err_1),h4

doc/Section_history.html

@@ -13,15 +13,17 @@ Section</A>
 
 <H3>13. Future and history 
 </H3>
-<P>This section lists features we are planning to add to LAMMPS, features
+<P>This section lists features we plan to add to LAMMPS, features of
-of previous versions of LAMMPS, and features of other parallel
+previous versions of LAMMPS, and features of other parallel molecular
-molecular dynamics codes I've distributed.
+dynamics codes our group has distributed.
 </P>
 13.1 <A HREF = "#hist_1">Coming attractions</A><BR>
 13.2 <A HREF = "#hist_2">Past versions</A> <BR>
 
 <HR>
 
+<HR>
+
 <H4><A NAME = "hist_1"></A>13.1 Coming attractions 
 </H4>
 <P>The <A HREF = "http://lammps.sandia.gov/future.html">Wish list link</A> on the

doc/Section_history.txt

@@ -10,13 +10,14 @@ Section"_Manual.html :c
 
 13. Future and history :h3
 
-This section lists features we are planning to add to LAMMPS, features
+This section lists features we plan to add to LAMMPS, features of
-of previous versions of LAMMPS, and features of other parallel
+previous versions of LAMMPS, and features of other parallel molecular
-molecular dynamics codes I've distributed.
+dynamics codes our group has distributed.
 
 13.1 "Coming attractions"_#hist_1
 13.2 "Past versions"_#hist_2 :all(b)
 
+:line
 :line
 
 13.1 Coming attractions :h4,link(hist_1)

doc/Section_howto.html

@@ -11,8 +11,7 @@
 
 <H3>6. How-to discussions 
 </H3>
-<P>The following sections describe how to use various options within
+<P>This section describes how to perform common tasks using LAMMPS.
-LAMMPS.
 </P>
 6.1 <A HREF = "#howto_1">Restarting a simulation</A><BR>
 6.2 <A HREF = "#howto_2">2d simulations</A><BR>
@@ -42,6 +41,8 @@ setup and run various kinds of simulations.
 </P>
 <HR>
 
+<HR>
+
 <A NAME = "howto_1"></A><H4>6.1 Restarting a simulation 
 </H4>
 <P>There are 3 ways to continue a long LAMMPS simulation.  Multiple

doc/Section_howto.txt

@@ -8,8 +8,7 @@
 
 6. How-to discussions :h3
 
-The following sections describe how to use various options within
+This section describes how to perform common tasks using LAMMPS.
-LAMMPS.
 
 6.1 "Restarting a simulation"_#howto_1
 6.2 "2d simulations"_#howto_2
@@ -37,6 +36,7 @@ The example input scripts included in the LAMMPS distribution and
 highlighted in "this section"_Section_example.html also show how to
 setup and run various kinds of simulations.
 
+:line
 :line
 
 6.1 Restarting a simulation :link(howto_1),h4

doc/Section_intro.html

@@ -11,10 +11,10 @@
 
 <H3>1. Introduction 
 </H3>
-<P>These sections provide an overview of what LAMMPS can and can't do,
+<P>This section provides an overview of what LAMMPS can and can't do,
-describe what it means for LAMMPS to be an open-source code, and
+describes what it means for LAMMPS to be an open-source code, and
-acknowledge the funding and people who have contributed to LAMMPS over
+acknowledges the funding and people who have contributed to LAMMPS
-the years.
+over the years.
 </P>
 1.1 <A HREF = "#intro_1">What is LAMMPS</A><BR>
 1.2 <A HREF = "#intro_2">LAMMPS features</A><BR>
@@ -24,6 +24,8 @@ the years.
 
 <HR>
 
+<HR>
+
 <A NAME = "intro_1"></A><H4>1.1 What is LAMMPS 
 </H4>
 <P>LAMMPS is a classical molecular dynamics code that models an ensemble

doc/Section_intro.txt

@@ -8,10 +8,10 @@
 
 1. Introduction :h3
 
-These sections provide an overview of what LAMMPS can and can't do,
+This section provides an overview of what LAMMPS can and can't do,
-describe what it means for LAMMPS to be an open-source code, and
+describes what it means for LAMMPS to be an open-source code, and
-acknowledge the funding and people who have contributed to LAMMPS over
+acknowledges the funding and people who have contributed to LAMMPS
-the years.
+over the years.
 
 1.1 "What is LAMMPS"_#intro_1
 1.2 "LAMMPS features"_#intro_2
@@ -19,6 +19,7 @@ the years.
 1.4 "Open source distribution"_#intro_4
 1.5 "Acknowledgments and citations"_#intro_5 :all(b)
 
+:line
 :line
 
 1.1 What is LAMMPS :link(intro_1),h4

doc/Section_modify.html

@@ -13,6 +13,24 @@ Section</A>
 
 <H3>10. Modifying & extending LAMMPS 
 </H3>
+<P>This section describes how to customize LAMMPS by modifying
+and extending its source code.
+</P>
+10.1 <A HREF = "#mod_1">Atom styles</A><BR>
+10.2 <A HREF = "#mod_2">Bond, angle, dihedral, improper potentials</A><BR>
+10.3 <A HREF = "#mod_3">Compute styles</A><BR>
+10.4 <A HREF = "#mod_4">Dump styles</A><BR>
+10.5 <A HREF = "#mod_5">Dump custom output options</A><BR>
+10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators,      temperature and pressure control, force constraints,      boundary conditions, diagnostic output, etc<BR>
+10.7 <A HREF = "mod_7">Input script commands</A><BR>
+10.8 <A HREF = "#mod_8">Kspace computations</A><BR>
+10.9 <A HREF = "#mod_9">Minimization styles</A><BR>
+10.10 <A HREF = "#mod_10">Pairwise potentials</A><BR>
+10.11 <A HREF = "#mod_11">Region styles</A><BR>
+10.12 <A HREF = "#mod_12">Thermodynamic output options</A><BR>
+10.13 <A HREF = "#mod_13">Variable options</A><BR>
+10.14 <A HREF = "#mod_14">Submitting new features for inclusion in LAMMPS</A> <BR>
+
 <P>LAMMPS is designed in a modular fashion so as to be easy to modify and
 extend with new functionality.  In fact, about 75% of its source code
 is files added in this fashion.
@@ -92,8 +110,6 @@ you can optionally define.
 thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
 below.
 </P>
-<HR>
-
 <P>Here are additional guidelines for modifying LAMMPS and adding new
 functionality:
 </P>
@@ -114,30 +130,10 @@ command.
 LAMMPS performance when it isn't used, send an email to the
 <A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.  We might be
 interested in adding it to the LAMMPS distribution.  See further
-details on this at the bottom of this page.  
+details on this at the bottom of this page. 
 </UL>
 <HR>
 
-<P>Here are the subsequent topics discussed below, most of which are new
-features that can be added in the manner just described:
-</P>
-10.1 <A HREF = "#mod_1">Atom styles</A><BR>
-10.2 <A HREF = "#mod_2">Bond, angle, dihedral, improper potentials</A><BR>
-10.3 <A HREF = "#mod_3">Compute styles</A><BR>
-10.4 <A HREF = "#mod_4">Dump styles</A><BR>
-10.5 <A HREF = "#mod_5">Dump custom output options</A><BR>
-10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators,      temperature and pressure control, force constraints,      boundary conditions, diagnostic output, etc<BR>
-10.7 <A HREF = "mod_7">Input script commands</A><BR>
-10.8 <A HREF = "#mod_8">Kspace computations</A><BR>
-10.9 <A HREF = "#mod_9">Minimization styles</A><BR>
-10.10 <A HREF = "#mod_10">Pairwise potentials</A><BR>
-10.11 <A HREF = "#mod_11">Region styles</A><BR>
-10.12 <A HREF = "#mod_12">Thermodynamic output options</A><BR>
-10.13 <A HREF = "#mod_13">Variable options</A><BR>
-10.14 <A HREF = "#mod_14">Submitting new features for inclusion in LAMMPS</A> <BR>
-
-<HR>
-
 <HR>
 
 <A NAME = "mod_1"></A><H4>10.1 Atom styles 

doc/Section_modify.txt

@@ -10,6 +10,26 @@ Section"_Section_python.html :c
 
 10. Modifying & extending LAMMPS :h3
 
+This section describes how to customize LAMMPS by modifying
+and extending its source code.
+
+10.1 "Atom styles"_#mod_1
+10.2 "Bond, angle, dihedral, improper potentials"_#mod_2
+10.3 "Compute styles"_#mod_3
+10.4 "Dump styles"_#mod_4
+10.5 "Dump custom output options"_#mod_5
+10.6 "Fix styles"_#mod_6 which include integrators, \
+     temperature and pressure control, force constraints, \
+     boundary conditions, diagnostic output, etc
+10.7 "Input script commands"_mod_7
+10.8 "Kspace computations"_#mod_8
+10.9 "Minimization styles"_#mod_9
+10.10 "Pairwise potentials"_#mod_10
+10.11 "Region styles"_#mod_11
+10.12 "Thermodynamic output options"_#mod_12
+10.13 "Variable options"_#mod_13
+10.14 "Submitting new features for inclusion in LAMMPS"_#mod_14 :all(b)
+
 LAMMPS is designed in a modular fashion so as to be easy to modify and
 extend with new functionality.  In fact, about 75% of its source code
 is files added in this fashion.
@@ -89,8 +109,6 @@ Additionally, new output options can be added directly to the
 thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
 below.
 
-:line
-
 Here are additional guidelines for modifying LAMMPS and adding new
 functionality:
 
@@ -111,29 +129,7 @@ If you add something you think is truly useful and doesn't impact
 LAMMPS performance when it isn't used, send an email to the
 "developers"_http://lammps.sandia.gov/authors.html.  We might be
 interested in adding it to the LAMMPS distribution.  See further
-details on this at the bottom of this page.  :l,ule
+details on this at the bottom of this page. :l,ule
-
-:line
-
-Here are the subsequent topics discussed below, most of which are new
-features that can be added in the manner just described:
-
-10.1 "Atom styles"_#mod_1
-10.2 "Bond, angle, dihedral, improper potentials"_#mod_2
-10.3 "Compute styles"_#mod_3
-10.4 "Dump styles"_#mod_4
-10.5 "Dump custom output options"_#mod_5
-10.6 "Fix styles"_#mod_6 which include integrators, \
-     temperature and pressure control, force constraints, \
-     boundary conditions, diagnostic output, etc
-10.7 "Input script commands"_mod_7
-10.8 "Kspace computations"_#mod_8
-10.9 "Minimization styles"_#mod_9
-10.10 "Pairwise potentials"_#mod_10
-10.11 "Region styles"_#mod_11
-10.12 "Thermodynamic output options"_#mod_12
-10.13 "Variable options"_#mod_13
-10.14 "Submitting new features for inclusion in LAMMPS"_#mod_14 :all(b)
 
 :line
 :line

doc/Section_packages.html

@@ -13,6 +13,12 @@ Section</A>
 
 <H3>4. Packages 
 </H3>
+<P>This section gives a quick overview of the add-on packages that extend
+LAMMPS functionality.
+</P>
+4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
+4.2 <A HREF = "#pkg_2">User packages</A> <BR>
+
 <P>LAMMPS includes many optional packages, which are groups of files that
 enable a specific set of features.  For example, force fields for
 molecular systems or granular systems are in packages.  You can see
@@ -28,9 +34,6 @@ between standard packages and user packages in LAMMPS.
 standard packages, just a one-line description is given.  For user
 packages, more details are provided.
 </P>
-4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
-4.2 <A HREF = "#pkg_2">User packages</A> <BR>
-
 <HR>
 
 <HR>

doc/Section_packages.txt

@@ -10,6 +10,12 @@ Section"_Section_accelerate.html :c
 
 4. Packages :h3
 
+This section gives a quick overview of the add-on packages that extend
+LAMMPS functionality.
+
+4.1 "Standard packages"_#pkg_1
+4.2 "User packages"_#pkg_2 :all(b)
+
 LAMMPS includes many optional packages, which are groups of files that
 enable a specific set of features.  For example, force fields for
 molecular systems or granular systems are in packages.  You can see
@@ -25,9 +31,6 @@ Below, the packages currently availabe in LAMMPS are listed.  For
 standard packages, just a one-line description is given.  For user
 packages, more details are provided.
 
-4.1 "Standard packages"_#pkg_1
-4.2 "User packages"_#pkg_2 :all(b)
-
 :line
 :line
 

doc/Section_python.html

@@ -11,6 +11,17 @@
 
 <H3>11. Python interface to LAMMPS 
 </H3>
+<P>This section describes how to build and use LAMMPS via a Python
+interface.
+</P>
+<UL><LI>11.1 <A HREF = "#py_1">Extending Python with a serial version of LAMMPS</A>
+<LI>11.2 <A HREF = "#py_2">Creating a shared MPI library</A>
+<LI>11.3 <A HREF = "#py_3">Extending Python with a parallel version of LAMMPS</A>
+<LI>11.4 <A HREF = "#py_4">Extending Python with MPI</A>
+<LI>11.5 <A HREF = "#py_5">Testing the Python-LAMMPS interface</A>
+<LI>11.6 <A HREF = "#py_6">Using LAMMPS from Python</A>
+<LI>11.7 <A HREF = "#py_7">Example Python scripts that use LAMMPS</A> 
+</UL>
 <P>The LAMMPS distribution includes some Python code in its python
 directory which wraps the library interface to LAMMPS.  This makes it
 is possible to run LAMMPS, invoke LAMMPS commands or give it an input
@@ -89,14 +100,6 @@ setup discussion.  The next to last sub-section describes the Python
 syntax used to invoke LAMMPS.  The last sub-section describes example
 Python scripts included in the python directory.
 </P>
-<UL><LI>11.1 <A HREF = "#py_1">Extending Python with a serial version of LAMMPS</A>
-<LI>11.2 <A HREF = "#py_2">Creating a shared MPI library</A>
-<LI>11.3 <A HREF = "#py_3">Extending Python with a parallel version of LAMMPS</A>
-<LI>11.4 <A HREF = "#py_4">Extending Python with MPI</A>
-<LI>11.5 <A HREF = "#py_5">Testing the Python-LAMMPS interface</A>
-<LI>11.6 <A HREF = "#py_6">Using LAMMPS from Python</A>
-<LI>11.7 <A HREF = "#py_7">Example Python scripts that use LAMMPS</A> 
-</UL>
 <P>Before proceeding, there are 2 items to note.
 </P>
 <P>(1) The provided Python wrapper for LAMMPS uses the amazing and

doc/Section_python.txt

@@ -8,6 +8,17 @@
 
 11. Python interface to LAMMPS :h3
 
+This section describes how to build and use LAMMPS via a Python
+interface.
+
+11.1 "Extending Python with a serial version of LAMMPS"_#py_1
+11.2 "Creating a shared MPI library"_#py_2
+11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
+11.4 "Extending Python with MPI"_#py_4
+11.5 "Testing the Python-LAMMPS interface"_#py_5
+11.6 "Using LAMMPS from Python"_#py_6
+11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
+
 The LAMMPS distribution includes some Python code in its python
 directory which wraps the library interface to LAMMPS.  This makes it
 is possible to run LAMMPS, invoke LAMMPS commands or give it an input
@@ -86,14 +97,6 @@ setup discussion.  The next to last sub-section describes the Python
 syntax used to invoke LAMMPS.  The last sub-section describes example
 Python scripts included in the python directory.
 
-11.1 "Extending Python with a serial version of LAMMPS"_#py_1
-11.2 "Creating a shared MPI library"_#py_2
-11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
-11.4 "Extending Python with MPI"_#py_4
-11.5 "Testing the Python-LAMMPS interface"_#py_5
-11.6 "Using LAMMPS from Python"_#py_6
-11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
-
 Before proceeding, there are 2 items to note.
 
 (1) The provided Python wrapper for LAMMPS uses the amazing and

doc/Section_start.html

@@ -25,6 +25,8 @@ experienced users.
 
 <HR>
 
+<HR>
+
 <H4><A NAME = "start_1"></A>2.1 What's in the LAMMPS distribution 
 </H4>
 <P>When you download LAMMPS you will need to unzip and untar the

doc/Section_start.txt

@@ -20,6 +20,7 @@ experienced users.
 2.7 "Screen output"_#start_7
 2.8 "Tips for users of previous versions"_#start_8 :all(b)
 
+:line
 :line
 
 2.1 What's in the LAMMPS distribution :h4,link(start_1)