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18
doc/Section_accelerate.html
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@ -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>

18
doc/Section_accelerate.txt
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@ -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

6
doc/Section_commands.html
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@ -11,8 +11,8 @@
<H3>3. Commands
</H3>
<P>This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
<P>This section describes how a LAMMPS input script is formatted and the
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),

5
doc/Section_commands.txt
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@ -8,8 +8,8 @@
3. Commands :h3
This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
This section describes how a LAMMPS input script is formatted and the
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

6
doc/Section_errors.html
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@ -13,8 +13,8 @@ Section</A>
<H3>12. Errors
</H3>
<P>This section describes the various kinds of errors you can encounter
when using LAMMPS.
<P>This section describes the errors you can encounter 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

5
doc/Section_errors.txt
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@ -10,13 +10,14 @@ Section"_Section_history.html :c
12. Errors :h3
This section describes the various kinds of errors you can encounter
when using LAMMPS.
This section describes the errors you can encounter 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

8
doc/Section_history.html
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@ -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
of previous versions of LAMMPS, and features of other parallel
molecular dynamics codes I've distributed.
<P>This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
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

7
doc/Section_history.txt
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@ -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
of previous versions of LAMMPS, and features of other parallel
molecular dynamics codes I've distributed.
This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
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)

5
doc/Section_howto.html
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@ -11,8 +11,7 @@
<H3>6. How-to discussions
</H3>
<P>The following sections describe how to use various options within
LAMMPS.
<P>This section describes how to perform common tasks using 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

4
doc/Section_howto.txt
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@ -8,8 +8,7 @@
6. How-to discussions :h3
The following sections describe how to use various options within
LAMMPS.
This section describes how to perform common tasks using 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

10
doc/Section_intro.html
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@ -11,10 +11,10 @@
<H3>1. Introduction
</H3>
<P>These sections provide an overview of what LAMMPS can and can't do,
describe what it means for LAMMPS to be an open-source code, and
acknowledge the funding and people who have contributed to LAMMPS over
the years.
<P>This section provides an overview of what LAMMPS can and can't do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
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

9
doc/Section_intro.txt
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@ -8,10 +8,10 @@
1. Introduction :h3
These sections provide an overview of what LAMMPS can and can't do,
describe what it means for LAMMPS to be an open-source code, and
acknowledge the funding and people who have contributed to LAMMPS over
the years.
This section provides an overview of what LAMMPS can and can't do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
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

42
doc/Section_modify.html
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@ -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

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doc/Section_modify.txt
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@ -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
: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)
details on this at the bottom of this page. :l,ule
:line
:line

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@ -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>

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@ -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

19
doc/Section_python.html
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@ -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

19
doc/Section_python.txt
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@ -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

2
doc/Section_start.html
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@ -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

1
doc/Section_start.txt
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@ -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)