This section describes various methods for improving LAMMPS +performance for different classes of problems running +on different kinds of machines. +
+5.1 OPT packageAccelerated versions of various pair_style, fixes, computes, and other commands have been added to LAMMPS, which will typically run faster than the @@ -74,12 +84,6 @@ compute, and kspace sections.
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 packageThis 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 scriptLAMMPS executes by reading commands from a input script (text file), diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 06c530c179..b767c220e6 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -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 diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 58ea10e3ff..b7fbbbba7a 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -13,8 +13,8 @@ Section
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 problemsIf two LAMMPS runs do not produce the same answer on different diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt index 2bf511d925..9c44470ab6 100644 --- a/doc/Section_errors.txt +++ b/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 -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 diff --git a/doc/Section_history.html b/doc/Section_history.html index 522e4e1220..d827db95e7 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -13,15 +13,17 @@ Section
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 attractionsThe Wish list link on the diff --git a/doc/Section_history.txt b/doc/Section_history.txt index 92600b7e22..2c65825370 100644 --- a/doc/Section_history.txt +++ b/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 -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) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 7f200f929e..ada3d46ade 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -11,8 +11,7 @@
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 simulationThere are 3 ways to continue a long LAMMPS simulation. Multiple diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 65131975fb..00da9985a4 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -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 diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 3b659cf8e7..815541a4b2 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -11,10 +11,10 @@
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 LAMMPSLAMMPS is a classical molecular dynamics code that models an ensemble diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 2ceb4f78d4..53158cc399 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -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 diff --git a/doc/Section_modify.html b/doc/Section_modify.html index 8e217b40fe..8a5604d169 100644 --- a/doc/Section_modify.html +++ b/doc/Section_modify.html @@ -13,6 +13,24 @@ Section
This section describes how to customize LAMMPS by modifying +and extending its source code. +
+10.1 Atom stylesLAMMPS 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.
-Here are additional guidelines for modifying LAMMPS and adding new functionality:
@@ -114,30 +130,10 @@ command. LAMMPS performance when it isn't used, send an email to the developers. 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.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 stylesThis section gives a quick overview of the add-on packages that extend +LAMMPS functionality. +
+4.1 Standard packagesLAMMPS 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.
-4.1 Standard packagesThis section describes how to build and use LAMMPS via a Python +interface. +
+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.
-Before proceeding, there are 2 items to note.
(1) The provided Python wrapper for LAMMPS uses the amazing and diff --git a/doc/Section_python.txt b/doc/Section_python.txt index 8f2aae4567..6a80a827b3 100644 --- a/doc/Section_python.txt +++ b/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 diff --git a/doc/Section_start.html b/doc/Section_start.html index ea3f0bf52f..4d64107295 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -25,6 +25,8 @@ experienced users.
When you download LAMMPS you will need to unzip and untar the diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 6bcb3900d9..c6c82e1eba 100644 --- a/doc/Section_start.txt +++ b/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)