forked from lijiext/lammps
refactor headline levels to result in a more structured PDF manual
This commit is contained in:
Axel Kohlmeyer
parent
f6c76e04b8
commit
1a402d4002
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@ -21,7 +21,7 @@ HAS_VIRTUALENV = YES
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endif
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SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
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SOURCES=$(filter-out src/lammps_commands.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
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SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
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OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
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.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
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@ -18,12 +18,10 @@
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:line
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<H1></H1>
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LAMMPS Documentation :c,h1
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16 Mar 2018 version :c,h2
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LAMMPS Documentation :c,h3
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16 Mar 2018 version :c,h4
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Version info: :h4
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Version info: :h3
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The LAMMPS "version" is the date when it was released, such as 1 May
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2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
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@ -8,7 +8,7 @@ Section"_Section_howto.html :c
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:line
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5. Accelerating LAMMPS performance :h3
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5. Accelerating LAMMPS performance :h2
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This section describes various methods for improving LAMMPS
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performance for different classes of problems running on different
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@ -41,7 +41,7 @@ compute nodes, on different hardware platforms.
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:line
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:line
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5.1 Measuring performance :h4,link(acc_1)
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5.1 Measuring performance :h3,link(acc_1)
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Before trying to make your simulation run faster, you should
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understand how it currently performs and where the bottlenecks are.
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@ -89,7 +89,7 @@ LAMMPS, to obtain synchronized timings.
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:line
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5.2 General strategies :h4,link(acc_2)
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5.2 General strategies :h3,link(acc_2)
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NOTE: this section 5.2 is still a work in progress
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@ -141,7 +141,7 @@ when using a barostat.
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:line
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5.3 Packages with optimized styles :h4,link(acc_3)
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5.3 Packages with optimized styles :h3,link(acc_3)
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Accelerated versions of various "pair_style"_pair_style.html,
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"fixes"_fix.html, "computes"_compute.html, and other commands have
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@ -325,7 +325,7 @@ restrictions :ul
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:line
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5.4 Comparison of various accelerator packages :h4,link(acc_4)
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5.4 Comparison of various accelerator packages :h3,link(acc_4)
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NOTE: this section still needs to be re-worked with additional KOKKOS
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and USER-INTEL information.
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@ -6,7 +6,7 @@
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:line
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3. Commands :h3
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3. Commands :h2
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This section describes how a LAMMPS input script is formatted and the
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input script commands used to define a LAMMPS simulation.
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@ -190,7 +190,7 @@ allowed, but that should be sufficient for most use cases.
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:line
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3.3 Input script structure :h4,link(cmd_3)
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3.3 Input script structure :h3,link(cmd_3)
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This section describes the structure of a typical LAMMPS input script.
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The "examples" directory in the LAMMPS distribution contains many
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@ -414,7 +414,7 @@ Input script control:
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:line
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3.5 Individual commands :h4,link(cmd_5),link(comm)
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3.5 Individual commands :h3,link(cmd_5),link(comm)
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This section lists all LAMMPS commands alphabetically, with a separate
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listing below of styles within certain commands. The "previous
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@ -537,7 +537,7 @@ package"_Section_start.html#start_3.
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:line
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Fix styles :h4
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Fix styles :h3
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See the "fix"_fix.html command for one-line descriptions of each style
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or click on the style itself for a full description. Some of the
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@ -751,7 +751,7 @@ package"_Section_start.html#start_3.
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:line
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Compute styles :h4
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Compute styles :h3
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See the "compute"_compute.html command for one-line descriptions of
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each style or click on the style itself for a full description. Some
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@ -894,7 +894,7 @@ package"_Section_start.html#start_3.
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:line
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Pair_style potentials :h4
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Pair_style potentials :h3
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See the "pair_style"_pair_style.html command for an overview of pair
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potentials. Click on the style itself for a full description. Many
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@ -1107,7 +1107,7 @@ package"_Section_start.html#start_3.
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:line
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Bond_style potentials :h4
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Bond_style potentials :h3
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See the "bond_style"_bond_style.html command for an overview of bond
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potentials. Click on the style itself for a full description. Some
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@ -1141,7 +1141,7 @@ package"_Section_start.html#start_3.
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:line
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Angle_style potentials :h4
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Angle_style potentials :h3
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See the "angle_style"_angle_style.html command for an overview of
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angle potentials. Click on the style itself for a full description.
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@ -1177,7 +1177,7 @@ package"_Section_start.html#start_3.
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:line
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Dihedral_style potentials :h4
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Dihedral_style potentials :h3
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See the "dihedral_style"_dihedral_style.html command for an overview
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of dihedral potentials. Click on the style itself for a full
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@ -1211,7 +1211,7 @@ package"_Section_start.html#start_3.
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:line
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Improper_style potentials :h4
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Improper_style potentials :h3
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See the "improper_style"_improper_style.html command for an overview
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of improper potentials. Click on the style itself for a full
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@ -1240,7 +1240,7 @@ package"_Section_start.html#start_3.
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:line
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Kspace solvers :h4
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Kspace solvers :h3
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See the "kspace_style"_kspace_style.html command for an overview of
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Kspace solvers. Click on the style itself for a full description.
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@ -8,7 +8,7 @@ Section"_Section_history.html :c
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:line
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12. Errors :h3
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12. Errors :h2
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This section describes the errors you can encounter when using LAMMPS,
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either conceptually, or as printed out by the program.
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@ -167,7 +167,7 @@ As a last resort, you can send an email directly to the
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:line
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12.3 Error & warning messages :h4,link(err_3)
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12.3 Error & warning messages :h3,link(err_3)
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These are two alphabetic lists of the "ERROR"_#error and
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"WARNING"_#warn messages LAMMPS prints out and the reason why. If the
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@ -186,7 +186,7 @@ packages"_Section_start.html#start_3 are not listed here. If such an
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error occurs and is not self-explanatory, you'll need to look in the
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source code or contact the author of the package.
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Errors: :h4,link(error)
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Errors: :h3,link(error)
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:dlb
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@ -11037,7 +11037,7 @@ Self-explanatory. :dd
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:dle
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Warnings: :h4,link(warn)
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Warnings: :h3,link(warn)
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:dlb
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@ -6,7 +6,7 @@
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:line
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7. Example problems :h3
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7. Example problems :h2
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The LAMMPS distribution includes an examples sub-directory with many
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sample problems. Many are 2d models that run quickly are are
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@ -46,7 +46,7 @@ Lists of both kinds of directories are given below.
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:line
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Lowercase directories :h4
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Lowercase directories :h3
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accelerate: run with various acceleration options (OpenMP, GPU, Phi)
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airebo: polyethylene with AIREBO potential
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@ -122,7 +122,7 @@ browser.
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:line
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Uppercase directories :h4
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Uppercase directories :h3
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ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
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COUPLE: examples of how to use LAMMPS as a library
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@ -8,7 +8,7 @@ Section"_Manual.html :c
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:line
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13. Future and history :h3
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13. Future and history :h2
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This section lists features we plan to add to LAMMPS, features of
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previous versions of LAMMPS, and features of other parallel molecular
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@ -20,7 +20,7 @@ dynamics codes our group has distributed.
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:line
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:line
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13.1 Coming attractions :h4,link(hist_1)
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13.1 Coming attractions :h3,link(hist_1)
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As of summer 2016 we are using the "LAMMPS project issue tracker
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on GitHub"_https://github.com/lammps/lammps/issues for keeping
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@ -46,7 +46,7 @@ if you want to have your suggestion added to the list.
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:line
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13.2 Past versions :h4,link(hist_2)
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13.2 Past versions :h3,link(hist_2)
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LAMMPS development began in the mid 1990s under a cooperative research
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& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
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@ -6,7 +6,7 @@
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:line
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6. How-to discussions :h3
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6. How-to discussions :h2
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This section describes how to perform common tasks using LAMMPS.
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@ -1058,7 +1058,7 @@ Example input scripts for these kinds of models are in the body,
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colloid, dipole, ellipse, line, peri, pour, and tri directories of the
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"examples directory"_Section_example.html in the LAMMPS distribution.
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Atom styles :h5
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Atom styles :h4
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There are several "atom styles"_atom_style.html that allow for
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definition of finite-size particles: sphere, dipole, ellipsoid, line,
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@ -1140,7 +1140,7 @@ ellipses. This means they have the same moment of inertia as the 3d
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object. When temperature is computed, the correct degrees of freedom
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are used for rotation in a 2d versus 3d system.
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Pair potentials :h5
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Pair potentials :h4
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When a system with finite-size particles is defined, the particles
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will only rotate and experience torque if the force field computes
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@ -1168,7 +1168,7 @@ Brownian and lubrication potentials are used with spherical particles.
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The line, tri, and body potentials are used with line segment,
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triangular, and body particles respectively.
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Time integration :h5
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Time integration :h4
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There are several fixes that perform time integration on finite-size
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spherical particles, meaning the integrators update the rotational
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@ -1204,7 +1204,7 @@ Note that for mixtures of point and finite-size particles, these
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integration fixes can only be used with "groups"_group.html which
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contain finite-size particles.
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Computes, thermodynamics, and dump output :h5
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Computes, thermodynamics, and dump output :h4
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There are several computes that calculate the temperature or
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rotational energy of spherical or ellipsoidal particles:
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@ -1236,7 +1236,7 @@ angular momentum, the quaternion, the torque, the end-point and
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corner-point coordinates (for line and tri particles), and
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sub-particle attributes of body particles.
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Rigid bodies composed of finite-size particles :h5
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Rigid bodies composed of finite-size particles :h4
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The "fix rigid"_fix_rigid.html command treats a collection of
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particles as a rigid body, computes its inertia tensor, sums the total
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@ -1319,7 +1319,7 @@ to output and the kind of data they operate on and produce:
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"Variables that generate values to output"_#variable
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"Summary table of output options and data flow between commands"_#table :ul
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Global/per-atom/local data :h5,link(global)
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Global/per-atom/local data :h4,link(global)
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Various output-related commands work with three different styles of
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data: global, per-atom, or local. A global datum is one or more
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@ -1329,7 +1329,7 @@ atom. Local datums are calculated by each processor based on the
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atoms it owns, but there may be zero or more per atom, e.g. a list of
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bond distances.
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Scalar/vector/array data :h5,link(scalar)
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Scalar/vector/array data :h4,link(scalar)
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Global, per-atom, and local datums can each come in three kinds: a
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single scalar value, a vector of values, or a 2d array of values. The
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@ -1352,7 +1352,7 @@ the dimension twice (array -> scalar). Thus a command that uses
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scalar values as input can typically also process elements of a vector
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or array.
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Thermodynamic output :h5,link(thermo)
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Thermodynamic output :h4,link(thermo)
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The frequency and format of thermodynamic output is set by the
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"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
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@ -1377,7 +1377,7 @@ intensive values; you can include a division by "natoms" in the
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formula if desired, to make an extensive calculation produce an
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intensive result.
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Dump file output :h5,link(dump)
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Dump file output :h4,link(dump)
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Dump file output is specified by the "dump"_dump.html and
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"dump_modify"_dump_modify.html commands. There are several
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@ -1401,7 +1401,7 @@ provides the values to be output. In each case, the compute or fix
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must generate local values for input to the "dump local"_dump.html
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command.
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Fixes that write output files :h5,link(fixoutput)
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Fixes that write output files :h4,link(fixoutput)
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Several fixes take various quantities as input and can write output
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files: "fix ave/time"_fix_ave_time.html, "fix
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@ -1455,7 +1455,7 @@ values for a specific atom. Thus the "fix print"_fix_print.html
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command is a means to output a wide variety of quantities separate
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from normal thermodynamic or dump file output.
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Computes that process output quantities :h5,link(computeoutput)
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Computes that process output quantities :h4,link(computeoutput)
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The "compute reduce"_compute_reduce.html and "compute
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reduce/region"_compute_reduce.html commands take one or more per-atom
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@ -1481,7 +1481,7 @@ info, etc) and stores the values in a local vector or array. These
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are produced as output values which can be used as input to other
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output commands.
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Fixes that process output quantities :h5,link(fixprocoutput)
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Fixes that process output quantities :h4,link(fixprocoutput)
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The "fix vector"_fix_vector.html command can create global vectors as
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output from global scalars as input, accumulating them one element at
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@ -1503,7 +1503,7 @@ including per-atom quantities calculated by a "compute"_compute.html,
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by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
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The output of this fix can be used as input to other output commands.
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Computes that generate values to output :h5,link(compute)
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Computes that generate values to output :h4,link(compute)
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Every "compute"_compute.html in LAMMPS produces either global or
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per-atom or local values. The values can be scalars or vectors or
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@ -1513,7 +1513,7 @@ describes what it produces. Computes that produce per-atom or local
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values have the word "atom" or "local" in their style name. Computes
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without the word "atom" or "local" produce global values.
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Fixes that generate values to output :h5,link(fix)
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Fixes that generate values to output :h4,link(fix)
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Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
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local values which can be accessed by other commands. The values can
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@ -1522,7 +1522,7 @@ using the other commands described in this section. The doc page for
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each fix command tells whether it produces any output quantities and
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describes them.
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Variables that generate values to output :h5,link(variable)
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Variables that generate values to output :h4,link(variable)
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"Variables"_variable.html defined in an input script can store one or
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more strings. But equal-style, vector-style, and atom-style or
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@ -1534,7 +1534,7 @@ computes, fixes, and other variables. The values generated by
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variables can be used as input to and thus output by the other
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commands described in this section.
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Summary table of output options and data flow between commands :h5,link(table)
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Summary table of output options and data flow between commands :h4,link(table)
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|
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This table summarizes the various commands that can be used for
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generating output from LAMMPS. Each command produces output data of
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@ -2264,7 +2264,7 @@ Here, each of the 3 kinds of chunk-related commands is briefly
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overviewed. Then some examples are given of how to compute different
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properties with chunk commands.
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Compute chunk/atom command: :h5
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Compute chunk/atom command: :h4
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This compute can assign atoms to chunks of various styles. Only atoms
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in the specified group and optional specified region are assigned to a
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@ -2303,7 +2303,7 @@ do this. You can also define a "per-atom variable"_variable.html in
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the input script that uses a formula to generate a chunk ID for each
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atom.
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Fix ave/chunk command: :h5
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Fix ave/chunk command: :h4
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|
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This fix takes the ID of a "compute
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chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
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|
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@ -2320,7 +2320,7 @@ values to be time-averaged in various ways, and output to a file. The
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fix produces a global array as output with one row of values per
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chunk.
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|
||||
Compute */chunk commands: :h5
|
||||
Compute */chunk commands: :h4
|
||||
|
||||
Currently the following computes operate on chunks of atoms to produce
|
||||
per-chunk values.
|
||||
|
|
@ -2365,7 +2365,7 @@ variables"_variable.html, like sum() and max(). E.g. to find the
|
|||
largest cluster or fastest diffusing molecule. :l
|
||||
:ule
|
||||
|
||||
Example calculations with chunks :h5
|
||||
Example calculations with chunks :h4
|
||||
|
||||
Here are examples using chunk commands to calculate various
|
||||
properties:
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
|
||||
:line
|
||||
|
||||
1. Introduction :h3
|
||||
1. Introduction :h2
|
||||
|
||||
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
|
||||
|
|
@ -97,7 +97,7 @@ favorite interatomic potential, boundary condition, or atom type, see
|
|||
"Section 10"_Section_modify.html, which describes how you can add
|
||||
it to LAMMPS.
|
||||
|
||||
General features :h5
|
||||
General features :h4
|
||||
|
||||
runs on a single processor or in parallel
|
||||
distributed-memory message-passing parallelism (MPI)
|
||||
|
|
@ -114,7 +114,7 @@ General features :h5
|
|||
build as library, invoke LAMMPS thru library interface or provided Python wrapper
|
||||
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
|
||||
|
||||
Particle and model types :h5
|
||||
Particle and model types :h4
|
||||
("atom style"_atom_style.html command)
|
||||
|
||||
atoms
|
||||
|
|
@ -130,7 +130,7 @@ Particle and model types :h5
|
|||
rigid collections of particles
|
||||
hybrid combinations of these :ul
|
||||
|
||||
Force fields :h5
|
||||
Force fields :h4
|
||||
("pair style"_pair_style.html, "bond style"_bond_style.html,
|
||||
"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
|
||||
"improper style"_improper_style.html, "kspace style"_kspace_style.html
|
||||
|
|
@ -169,7 +169,7 @@ commands)
|
|||
potentials can be used in one simulation
|
||||
overlaid potentials: superposition of multiple pair potentials :ul
|
||||
|
||||
Atom creation :h5
|
||||
Atom creation :h4
|
||||
("read_data"_read_data.html, "lattice"_lattice.html,
|
||||
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
|
||||
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
|
||||
|
|
@ -180,7 +180,7 @@ Atom creation :h5
|
|||
replicate existing atoms multiple times
|
||||
displace atoms :ul
|
||||
|
||||
Ensembles, constraints, and boundary conditions :h5
|
||||
Ensembles, constraints, and boundary conditions :h4
|
||||
("fix"_fix.html command)
|
||||
|
||||
2d or 3d systems
|
||||
|
|
@ -198,7 +198,7 @@ Ensembles, constraints, and boundary conditions :h5
|
|||
non-equilibrium molecular dynamics (NEMD)
|
||||
variety of additional boundary conditions and constraints :ul
|
||||
|
||||
Integrators :h5
|
||||
Integrators :h4
|
||||
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
|
||||
|
||||
velocity-Verlet integrator
|
||||
|
|
@ -208,11 +208,11 @@ Integrators :h5
|
|||
rRESPA hierarchical timestepping
|
||||
rerun command for post-processing of dump files :ul
|
||||
|
||||
Diagnostics :h5
|
||||
Diagnostics :h4
|
||||
|
||||
see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
|
||||
|
||||
Output :h5
|
||||
Output :h4
|
||||
("dump"_dump.html, "restart"_restart.html commands)
|
||||
|
||||
log file of thermodynamic info
|
||||
|
|
@ -225,14 +225,14 @@ Output :h5
|
|||
time averaging of system-wide quantities
|
||||
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
|
||||
|
||||
Multi-replica models :h5
|
||||
Multi-replica models :h4
|
||||
|
||||
"nudged elastic band"_neb.html
|
||||
"parallel replica dynamics"_prd.html
|
||||
"temperature accelerated dynamics"_tad.html
|
||||
"parallel tempering"_temper.html
|
||||
|
||||
Pre- and post-processing :h5
|
||||
Pre- and post-processing :h4
|
||||
|
||||
Various pre- and post-processing serial tools are packaged
|
||||
with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
|
||||
|
|
@ -247,7 +247,7 @@ Pizza.py WWW site"_pizza. :l
|
|||
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
|
||||
:link(python,http://www.python.org)
|
||||
|
||||
Specialized features :h5
|
||||
Specialized features :h4
|
||||
|
||||
LAMMPS can be built with optional packages which implement a variety
|
||||
of additional capabilities. An overview of all the packages is "given
|
||||
|
|
@ -468,7 +468,7 @@ encouraged. :l
|
|||
|
||||
:line
|
||||
|
||||
1.5 Acknowledgments and citations :h4,link(intro_5)
|
||||
1.5 Acknowledgments and citations :h3,link(intro_5)
|
||||
|
||||
LAMMPS development has been funded by the "US Department of
|
||||
Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ Section"_Section_python.html :c
|
|||
|
||||
:line
|
||||
|
||||
10. Modifying & extending LAMMPS :h3
|
||||
10. Modifying & extending LAMMPS :h2
|
||||
|
||||
This section describes how to customize LAMMPS by modifying
|
||||
and extending its source code.
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ Section"_Section_accelerate.html :c
|
|||
|
||||
:line
|
||||
|
||||
4. Packages :h3
|
||||
4. Packages :h2
|
||||
|
||||
This section gives an overview of the optional packages that extend
|
||||
LAMMPS functionality with instructions on how to build LAMMPS with
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
|
||||
:line
|
||||
|
||||
8. Performance & scalability :h3
|
||||
8. Performance & scalability :h2
|
||||
|
||||
Current LAMMPS performance is discussed on the Benchmarks page of the
|
||||
"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
|
||||
:line
|
||||
|
||||
11. Python interface to LAMMPS :h3
|
||||
11. Python interface to LAMMPS :h2
|
||||
|
||||
LAMMPS can work together with Python in three ways. First, Python can
|
||||
wrap LAMMPS through the "LAMMPS library
|
||||
|
|
@ -443,7 +443,7 @@ If an error occurs, carefully go thru the steps in "Section
|
|||
library and about insuring Python can find the necessary two files
|
||||
it needs.
|
||||
|
||||
[Test LAMMPS and Python in serial:] :h5
|
||||
[Test LAMMPS and Python in serial:] :h4
|
||||
|
||||
To run a LAMMPS test in serial, type these lines into Python
|
||||
interactively from the bench directory:
|
||||
|
|
@ -462,7 +462,7 @@ typed something like:
|
|||
|
||||
lmp_g++ -in in.lj :pre
|
||||
|
||||
[Test LAMMPS and Python in parallel:] :h5
|
||||
[Test LAMMPS and Python in parallel:] :h4
|
||||
|
||||
To run LAMMPS in parallel, assuming you have installed the
|
||||
"PyPar"_https://github.com/daleroberts/pypar package as discussed
|
||||
|
|
@ -510,7 +510,7 @@ described in the PyPar documentation. The last line of your Python
|
|||
script should be pypar.finalize(), to insure MPI is shut down
|
||||
correctly.
|
||||
|
||||
[Running Python scripts:] :h5
|
||||
[Running Python scripts:] :h4
|
||||
|
||||
Note that any Python script (not just for LAMMPS) can be invoked in
|
||||
one of several ways:
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
|
||||
:line
|
||||
|
||||
2. Getting Started :h3
|
||||
2. Getting Started :h2
|
||||
|
||||
This section describes how to build and run LAMMPS, for both new and
|
||||
experienced users.
|
||||
|
|
@ -22,7 +22,7 @@ experienced users.
|
|||
|
||||
:line
|
||||
|
||||
2.1 What's in the LAMMPS distribution :h4,link(start_1)
|
||||
2.1 What's in the LAMMPS distribution :h3,link(start_1)
|
||||
|
||||
When you download a LAMMPS tarball you will need to unzip and untar
|
||||
the downloaded file with the following commands, after placing the
|
||||
|
|
@ -64,7 +64,7 @@ launch a LAMMPS Windows executable on a Windows box.
|
|||
|
||||
:line
|
||||
|
||||
2.2 Making LAMMPS :h4,link(start_2)
|
||||
2.2 Making LAMMPS :h3,link(start_2)
|
||||
|
||||
This section has the following sub-sections:
|
||||
|
||||
|
|
@ -77,7 +77,7 @@ This section has the following sub-sections:
|
|||
|
||||
:line
|
||||
|
||||
Read this first :h5,link(start_2_1)
|
||||
Read this first :h4,link(start_2_1)
|
||||
|
||||
If you want to avoid building LAMMPS yourself, read the preceding
|
||||
section about options available for downloading and installing
|
||||
|
|
@ -148,9 +148,9 @@ include it in the LAMMPS distribution.
|
|||
|
||||
:line
|
||||
|
||||
Steps to build a LAMMPS executable :h5,link(start_2_2)
|
||||
Steps to build a LAMMPS executable :h4,link(start_2_2)
|
||||
|
||||
Step 0 :h6
|
||||
Step 0 :h5
|
||||
|
||||
The src directory contains the C++ source and header files for LAMMPS.
|
||||
It also contains a top-level Makefile and a MAKE sub-directory with
|
||||
|
|
@ -198,7 +198,7 @@ Note that by default only a few of LAMMPS optional packages are
|
|||
installed. To build LAMMPS with optional packages, see "this
|
||||
section"_#start_3 below.
|
||||
|
||||
Step 1 :h6
|
||||
Step 1 :h5
|
||||
|
||||
If Step 0 did not work, you will need to create a low-level Makefile
|
||||
for your machine, like Makefile.foo. You should make a copy of an
|
||||
|
|
@ -209,13 +209,13 @@ the first line, the "compiler/linker settings" section, and the
|
|||
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
|
||||
updates.
|
||||
|
||||
Step 2 :h6
|
||||
Step 2 :h5
|
||||
|
||||
Change the first line of Makefile.foo to list the word "foo" after the
|
||||
"#", and whatever other options it will set. This is the line you
|
||||
will see if you just type "make".
|
||||
|
||||
Step 3 :h6
|
||||
Step 3 :h5
|
||||
|
||||
The "compiler/linker settings" section lists compiler and linker
|
||||
settings for your C++ compiler, including optimization flags. You can
|
||||
|
|
@ -244,7 +244,7 @@ first time on a new platform, a long list of *.d files will be printed
|
|||
out rapidly. This is not an error; it is the Makefile doing its
|
||||
normal creation of dependencies.
|
||||
|
||||
Step 4 :h6
|
||||
Step 4 :h5
|
||||
|
||||
The "system-specific settings" section has several parts. Note that
|
||||
if you change any -D setting in this section, you should do a full
|
||||
|
|
@ -345,7 +345,7 @@ platforms. The -DPACK_ARRAY setting is the default. See the
|
|||
"kspace_style"_kspace_style.html command for info about PPPM. See
|
||||
Step 6 below for info about building LAMMPS with an FFT library.
|
||||
|
||||
Step 5 :h6
|
||||
Step 5 :h5
|
||||
|
||||
The 3 MPI variables are used to specify an MPI library to build LAMMPS
|
||||
with. Note that you do not need to set these if you use the MPI
|
||||
|
|
@ -401,7 +401,7 @@ Note that the ANSI-standard function clock() rolls over after an hour
|
|||
or so, and is therefore insufficient for timing long LAMMPS
|
||||
simulations.
|
||||
|
||||
Step 6 :h6
|
||||
Step 6 :h5
|
||||
|
||||
The 3 FFT variables allow you to specify an FFT library which LAMMPS
|
||||
uses (for performing 1d FFTs) when running the particle-particle
|
||||
|
|
@ -482,7 +482,7 @@ double-precision library (libdfftw.a and not the default libfftw.a),
|
|||
then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
|
||||
-ldfftw to use double-precision FFTs.
|
||||
|
||||
Step 7 :h6
|
||||
Step 7 :h5
|
||||
|
||||
The 3 JPG variables allow you to specify a JPEG and/or PNG library
|
||||
which LAMMPS uses when writing out JPEG or PNG files via the "dump
|
||||
|
|
@ -505,13 +505,13 @@ find it.
|
|||
As before, if these header and library files are in the usual place on
|
||||
your machine, you may not need to set these variables.
|
||||
|
||||
Step 8 :h6
|
||||
Step 8 :h5
|
||||
|
||||
Note that by default only a few of LAMMPS optional packages are
|
||||
installed. To build LAMMPS with optional packages, see "this
|
||||
section"_#start_3 below, before proceeding to Step 9.
|
||||
|
||||
Step 9 :h6
|
||||
Step 9 :h5
|
||||
|
||||
That's it. Once you have a correct Makefile.foo, and you have
|
||||
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
|
||||
|
|
@ -530,7 +530,7 @@ You should get the executable lmp_foo when the build is complete.
|
|||
|
||||
:line
|
||||
|
||||
Errors that can occur when making LAMMPS :h5 :link(start_2_3)
|
||||
Errors that can occur when making LAMMPS :h4 :link(start_2_3)
|
||||
|
||||
If an error occurs when building LAMMPS, the compiler or linker will
|
||||
state very explicitly what the problem is. The error message should
|
||||
|
|
@ -567,21 +567,21 @@ above in Step 4.
|
|||
|
||||
:line
|
||||
|
||||
Additional build tips :h5,link(start_2_4)
|
||||
Additional build tips :h4,link(start_2_4)
|
||||
|
||||
Building LAMMPS for multiple platforms. :h6
|
||||
Building LAMMPS for multiple platforms. :h5
|
||||
|
||||
You can make LAMMPS for multiple platforms from the same src
|
||||
directory. Each target creates its own object sub-directory called
|
||||
Obj_target where it stores the system-specific *.o files.
|
||||
|
||||
Cleaning up. :h6
|
||||
Cleaning up. :h5
|
||||
|
||||
Typing "make clean-all" or "make clean-machine" will delete *.o object
|
||||
files created when LAMMPS is built, for either all builds or for a
|
||||
particular machine.
|
||||
|
||||
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
|
||||
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h5
|
||||
|
||||
As explained above, any of these 3 settings can be specified on the
|
||||
LMP_INC line in your low-level src/MAKE/Makefile.foo.
|
||||
|
|
@ -631,14 +631,14 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
|
|||
|
||||
:line
|
||||
|
||||
Building for a Mac :h5,link(start_2_5)
|
||||
Building for a Mac :h4,link(start_2_5)
|
||||
|
||||
OS X is a derivative of BSD Unix, so it should just work. See the
|
||||
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
|
||||
|
||||
:line
|
||||
|
||||
Building for Windows :h5,link(start_2_6)
|
||||
Building for Windows :h4,link(start_2_6)
|
||||
|
||||
If you want to build a Windows version of LAMMPS, you can build it
|
||||
yourself, but it may require some effort. LAMMPS expects a Unix-like
|
||||
|
|
@ -678,7 +678,7 @@ examples, but no source code.
|
|||
|
||||
:line
|
||||
|
||||
2.3 Making LAMMPS with optional packages :h4,link(start_3)
|
||||
2.3 Making LAMMPS with optional packages :h3,link(start_3)
|
||||
|
||||
This section has the following sub-sections:
|
||||
|
||||
|
|
@ -688,7 +688,7 @@ This section has the following sub-sections:
|
|||
|
||||
:line
|
||||
|
||||
Package basics: :h5,link(start_3_1)
|
||||
Package basics: :h4,link(start_3_1)
|
||||
|
||||
The source code for LAMMPS is structured as a set of core files which
|
||||
are always included, plus optional packages. Packages are groups of
|
||||
|
|
@ -719,7 +719,7 @@ known to your executable, and immediately exit.
|
|||
|
||||
:line
|
||||
|
||||
Including/excluding packages :h5,link(start_3_2)
|
||||
Including/excluding packages :h4,link(start_3_2)
|
||||
|
||||
To use (or not use) a package you must install it (or un-install it)
|
||||
before building LAMMPS. From the src directory, this is as simple as:
|
||||
|
|
@ -823,7 +823,7 @@ options.
|
|||
|
||||
:line
|
||||
|
||||
Packages that require extra libraries :h5,link(start_3_3)
|
||||
Packages that require extra libraries :h4,link(start_3_3)
|
||||
|
||||
A few of the standard and user packages require extra libraries. See
|
||||
"Section 4"_Section_packages.html for two tables of packages which
|
||||
|
|
@ -925,7 +925,7 @@ Makefile.opt :ul
|
|||
|
||||
:line
|
||||
|
||||
2.4 Building LAMMPS as a library :h4,link(start_4)
|
||||
2.4 Building LAMMPS as a library :h3,link(start_4)
|
||||
|
||||
LAMMPS can be built as either a static or shared library, which can
|
||||
then be called from another application or a scripting language. See
|
||||
|
|
@ -933,7 +933,7 @@ then be called from another application or a scripting language. See
|
|||
LAMMPS to other codes. See "this section"_Section_python.html for
|
||||
more info on wrapping and running LAMMPS from Python.
|
||||
|
||||
Static library :h5
|
||||
Static library :h4
|
||||
|
||||
To build LAMMPS as a static library (*.a file on Linux), type
|
||||
|
||||
|
|
@ -947,7 +947,7 @@ will create the file liblammps_foo.a which another application can
|
|||
link to. It will also create a soft link liblammps.a, which will
|
||||
point to the most recently built static library.
|
||||
|
||||
Shared library :h5
|
||||
Shared library :h4
|
||||
|
||||
To build LAMMPS as a shared library (*.so file on Linux), which can be
|
||||
dynamically loaded, e.g. from Python, type
|
||||
|
|
@ -1004,7 +1004,7 @@ You may need to use "sudo make install" in place of the last line if
|
|||
you do not have write privileges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
|
||||
[Additional requirement for using a shared library:] :h5
|
||||
[Additional requirement for using a shared library:] :h4
|
||||
|
||||
The operating system finds shared libraries to load at run-time using
|
||||
the environment variable LD_LIBRARY_PATH. So you may wish to copy the
|
||||
|
|
@ -1019,7 +1019,7 @@ For the csh or tcsh shells, you would add something like this to your
|
|||
|
||||
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
|
||||
|
||||
Calling the LAMMPS library :h5
|
||||
Calling the LAMMPS library :h4
|
||||
|
||||
Either flavor of library (static or shared) allows one or more LAMMPS
|
||||
objects to be instantiated from the calling program.
|
||||
|
|
@ -1047,7 +1047,7 @@ interface and how to extend it for your needs.
|
|||
|
||||
:line
|
||||
|
||||
2.5 Running LAMMPS :h4,link(start_5)
|
||||
2.5 Running LAMMPS :h3,link(start_5)
|
||||
|
||||
By default, LAMMPS runs by reading commands from standard input. Thus
|
||||
if you run the LAMMPS executable by itself, e.g.
|
||||
|
|
@ -1193,7 +1193,7 @@ more processors or setup a smaller problem.
|
|||
|
||||
:line
|
||||
|
||||
2.6 Command-line options :h4,link(start_6)
|
||||
2.6 Command-line options :h3,link(start_6)
|
||||
|
||||
At run time, LAMMPS recognizes several optional command-line switches
|
||||
which may be used in any order. Either the full word or a one-or-two
|
||||
|
|
@ -1623,7 +1623,7 @@ negative numeric value. It is OK if the first value1 starts with a
|
|||
|
||||
:line
|
||||
|
||||
2.7 LAMMPS screen output :h4,link(start_7)
|
||||
2.7 LAMMPS screen output :h3,link(start_7)
|
||||
|
||||
As LAMMPS reads an input script, it prints information to both the
|
||||
screen and a log file about significant actions it takes to setup a
|
||||
|
|
@ -1779,7 +1779,7 @@ communication, roughly 75% in the example above.
|
|||
|
||||
:line
|
||||
|
||||
2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
|
||||
2.8 Tips for users of previous LAMMPS versions :h3,link(start_8)
|
||||
|
||||
The current C++ began with a complete rewrite of LAMMPS 2001, which
|
||||
was written in F90. Features of earlier versions of LAMMPS are listed
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ Section"_Section_modify.html :c
|
|||
|
||||
:line
|
||||
|
||||
9. Additional tools :h3
|
||||
9. Additional tools :h2
|
||||
|
||||
LAMMPS is designed to be a computational kernel for performing
|
||||
molecular dynamics computations. Additional pre- and post-processing
|
||||
|
|
@ -75,7 +75,7 @@ own sub-directories with their own Makefiles and/or README files.
|
|||
|
||||
:line
|
||||
|
||||
amber2lmp tool :h4,link(amber)
|
||||
amber2lmp tool :h3,link(amber)
|
||||
|
||||
The amber2lmp sub-directory contains two Python scripts for converting
|
||||
files back-and-forth between the AMBER MD code and LAMMPS. See the
|
||||
|
|
@ -90,7 +90,7 @@ necessary modifications yourself.
|
|||
|
||||
:line
|
||||
|
||||
binary2txt tool :h4,link(binary)
|
||||
binary2txt tool :h3,link(binary)
|
||||
|
||||
The file binary2txt.cpp converts one or more binary LAMMPS dump file
|
||||
into ASCII text files. The syntax for running the tool is
|
||||
|
|
@ -103,7 +103,7 @@ since binary files are not compatible across all platforms.
|
|||
|
||||
:line
|
||||
|
||||
ch2lmp tool :h4,link(charmm)
|
||||
ch2lmp tool :h3,link(charmm)
|
||||
|
||||
The ch2lmp sub-directory contains tools for converting files
|
||||
back-and-forth between the CHARMM MD code and LAMMPS.
|
||||
|
|
@ -128,7 +128,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
|
|||
|
||||
:line
|
||||
|
||||
chain tool :h4,link(chain)
|
||||
chain tool :h3,link(chain)
|
||||
|
||||
The file chain.f creates a LAMMPS data file containing bead-spring
|
||||
polymer chains and/or monomer solvent atoms. It uses a text file
|
||||
|
|
@ -145,7 +145,7 @@ system for the "chain benchmark"_Section_perf.html.
|
|||
|
||||
:line
|
||||
|
||||
colvars tools :h4,link(colvars)
|
||||
colvars tools :h3,link(colvars)
|
||||
|
||||
The colvars directory contains a collection of tools for postprocessing
|
||||
data produced by the colvars collective variable library.
|
||||
|
|
@ -167,7 +167,7 @@ gmail.com) at ICTP, Italy.
|
|||
|
||||
:line
|
||||
|
||||
createatoms tool :h4,link(createatoms)
|
||||
createatoms tool :h3,link(createatoms)
|
||||
|
||||
The tools/createatoms directory contains a Fortran program called
|
||||
createAtoms.f which can generate a variety of interesting crystal
|
||||
|
|
@ -180,7 +180,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
|
|||
|
||||
:line
|
||||
|
||||
doxygen tool :h4,link(doxygen)
|
||||
doxygen tool :h3,link(doxygen)
|
||||
|
||||
The tools/doxygen directory contains a shell script called
|
||||
doxygen.sh which can generate a call graph and API lists using
|
||||
|
|
@ -192,7 +192,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
|
|||
|
||||
:line
|
||||
|
||||
drude tool :h4,link(drude)
|
||||
drude tool :h3,link(drude)
|
||||
|
||||
The tools/drude directory contains a Python script called
|
||||
polarizer.py which can add Drude oscillators to a LAMMPS
|
||||
|
|
@ -205,7 +205,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
|
|||
|
||||
:line
|
||||
|
||||
eam database tool :h4,link(eamdb)
|
||||
eam database tool :h3,link(eamdb)
|
||||
|
||||
The tools/eam_database directory contains a Fortran program that will
|
||||
generate EAM alloy setfl potential files for any combination of 16
|
||||
|
|
@ -221,7 +221,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
|
|||
|
||||
:line
|
||||
|
||||
eam generate tool :h4,link(eamgn)
|
||||
eam generate tool :h3,link(eamgn)
|
||||
|
||||
The tools/eam_generate directory contains several one-file C programs
|
||||
that convert an analytic formula into a tabulated "embedded atom
|
||||
|
|
@ -234,7 +234,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
|
|||
|
||||
:line
|
||||
|
||||
eff tool :h4,link(eff)
|
||||
eff tool :h3,link(eff)
|
||||
|
||||
The tools/eff directory contains various scripts for generating
|
||||
structures and post-processing output for simulations using the
|
||||
|
|
@ -245,7 +245,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
|
|||
|
||||
:line
|
||||
|
||||
emacs tool :h4,link(emacs)
|
||||
emacs tool :h3,link(emacs)
|
||||
|
||||
The tools/emacs directory contains a Lips add-on file for Emacs that
|
||||
enables a lammps-mode for editing of input scripts when using Emacs,
|
||||
|
|
@ -256,7 +256,7 @@ These tools were provided by Aidan Thompson at Sandia
|
|||
|
||||
:line
|
||||
|
||||
fep tool :h4,link(fep)
|
||||
fep tool :h3,link(fep)
|
||||
|
||||
The tools/fep directory contains Python scripts useful for
|
||||
post-processing results from performing free-energy perturbation
|
||||
|
|
@ -269,7 +269,7 @@ See README file in the tools/fep directory.
|
|||
|
||||
:line
|
||||
|
||||
i-pi tool :h4,link(ipi)
|
||||
i-pi tool :h3,link(ipi)
|
||||
|
||||
The tools/i-pi directory contains a version of the i-PI package, with
|
||||
all the LAMMPS-unrelated files removed. It is provided so that it can
|
||||
|
|
@ -286,7 +286,7 @@ calculations with LAMMPS.
|
|||
|
||||
:line
|
||||
|
||||
ipp tool :h4,link(ipp)
|
||||
ipp tool :h3,link(ipp)
|
||||
|
||||
The tools/ipp directory contains a Perl script ipp which can be used
|
||||
to facilitate the creation of a complicated file (say, a lammps input
|
||||
|
|
@ -300,7 +300,7 @@ tools/createatoms tool's input file.
|
|||
|
||||
:line
|
||||
|
||||
kate tool :h4,link(kate)
|
||||
kate tool :h3,link(kate)
|
||||
|
||||
The file in the tools/kate directory is an add-on to the Kate editor
|
||||
in the KDE suite that allow syntax highlighting of LAMMPS input
|
||||
|
|
@ -311,7 +311,7 @@ The file was provided by Alessandro Luigi Sellerio
|
|||
|
||||
:line
|
||||
|
||||
lmp2arc tool :h4,link(arc)
|
||||
lmp2arc tool :h3,link(arc)
|
||||
|
||||
The lmp2arc sub-directory contains a tool for converting LAMMPS output
|
||||
files to the format for Accelrys' Insight MD code (formerly
|
||||
|
|
@ -327,7 +327,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
|
|||
|
||||
:line
|
||||
|
||||
lmp2cfg tool :h4,link(cfg)
|
||||
lmp2cfg tool :h3,link(cfg)
|
||||
|
||||
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
|
||||
files into a series of *.cfg files which can be read into the
|
||||
|
|
@ -338,7 +338,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
|
|||
|
||||
:line
|
||||
|
||||
matlab tool :h4,link(matlab)
|
||||
matlab tool :h3,link(matlab)
|
||||
|
||||
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
|
||||
post-processing LAMMPS output. The scripts include readers for log
|
||||
|
|
@ -356,7 +356,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
|
|||
|
||||
:line
|
||||
|
||||
micelle2d tool :h4,link(micelle)
|
||||
micelle2d tool :h3,link(micelle)
|
||||
|
||||
The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
|
|
@ -373,7 +373,7 @@ definition file. This tool was used to create the system for the
|
|||
|
||||
:line
|
||||
|
||||
moltemplate tool :h4,link(moltemplate)
|
||||
moltemplate tool :h3,link(moltemplate)
|
||||
|
||||
The moltemplate sub-directory contains a Python-based tool for
|
||||
building molecular systems based on a text-file description, and
|
||||
|
|
@ -387,7 +387,7 @@ supports it. It has its own WWW page at
|
|||
|
||||
:line
|
||||
|
||||
msi2lmp tool :h4,link(msi)
|
||||
msi2lmp tool :h3,link(msi)
|
||||
|
||||
The msi2lmp sub-directory contains a tool for creating LAMMPS template
|
||||
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
|
||||
|
|
@ -404,7 +404,7 @@ See the README file in the tools/msi2lmp folder for more information.
|
|||
|
||||
:line
|
||||
|
||||
phonon tool :h4,link(phonon)
|
||||
phonon tool :h3,link(phonon)
|
||||
|
||||
The phonon sub-directory contains a post-processing tool useful for
|
||||
analyzing the output of the "fix phonon"_fix_phonon.html command in
|
||||
|
|
@ -419,7 +419,7 @@ University.
|
|||
|
||||
:line
|
||||
|
||||
polybond tool :h4,link(polybond)
|
||||
polybond tool :h3,link(polybond)
|
||||
|
||||
The polybond sub-directory contains a Python-based tool useful for
|
||||
performing "programmable polymer bonding". The Python file
|
||||
|
|
@ -433,7 +433,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
|
|||
|
||||
:line
|
||||
|
||||
pymol_asphere tool :h4,link(pymol)
|
||||
pymol_asphere tool :h3,link(pymol)
|
||||
|
||||
The pymol_asphere sub-directory contains a tool for converting a
|
||||
LAMMPS dump file that contains orientation info for ellipsoidal
|
||||
|
|
@ -451,7 +451,7 @@ This tool was written by Mike Brown at Sandia.
|
|||
|
||||
:line
|
||||
|
||||
python tool :h4,link(pythontools)
|
||||
python tool :h3,link(pythontools)
|
||||
|
||||
The python sub-directory contains several Python scripts
|
||||
that perform common LAMMPS post-processing tasks, such as:
|
||||
|
|
@ -467,7 +467,7 @@ README for more info on Pizza.py and how to use these scripts.
|
|||
|
||||
:line
|
||||
|
||||
reax tool :h4,link(reax_tool)
|
||||
reax tool :h3,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alond codes that can
|
||||
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
|
||||
|
|
@ -478,7 +478,7 @@ These tools were written by Aidan Thompson at Sandia.
|
|||
|
||||
:line
|
||||
|
||||
smd tool :h4,link(smd)
|
||||
smd tool :h3,link(smd)
|
||||
|
||||
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
|
||||
Makefile which can be compiled and used to convert triangle output
|
||||
|
|
@ -494,7 +494,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
|
|||
|
||||
:line
|
||||
|
||||
vim tool :h4,link(vim)
|
||||
vim tool :h3,link(vim)
|
||||
|
||||
The files in the tools/vim directory are add-ons to the VIM editor
|
||||
that allow easier editing of LAMMPS input scripts. See the README.txt
|
||||
|
|
@ -505,7 +505,7 @@ ziegenhain.com)
|
|||
|
||||
:line
|
||||
|
||||
xmgrace tool :h4,link(xmgrace)
|
||||
xmgrace tool :h3,link(xmgrace)
|
||||
|
||||
The files in the tools/xmgrace directory can be used to plot the
|
||||
thermodynamic data in LAMMPS log files via the xmgrace plotting
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
|
||||
:line
|
||||
|
||||
Body particles :h1
|
||||
Body particles :h2
|
||||
|
||||
[Overview:]
|
||||
|
||||
|
|
|
|||
|
|
@ -26,34 +26,26 @@ tutorial_drude.html
|
|||
tutorial_github.html
|
||||
tutorial_pylammps.html
|
||||
|
||||
lammps_support.html
|
||||
body.html
|
||||
manifolds.html
|
||||
|
||||
lammps_commands.html
|
||||
angle_coeff.html
|
||||
angle_style.html
|
||||
atom_modify.html
|
||||
atom_style.html
|
||||
balance.html
|
||||
bond_coeff.html
|
||||
bond_style.html
|
||||
bond_write.html
|
||||
boundary.html
|
||||
box.html
|
||||
change_box.html
|
||||
clear.html
|
||||
comm_modify.html
|
||||
comm_style.html
|
||||
compute.html
|
||||
compute_modify.html
|
||||
create_atoms.html
|
||||
create_bonds.html
|
||||
create_box.html
|
||||
delete_atoms.html
|
||||
delete_bonds.html
|
||||
dielectric.html
|
||||
dihedral_coeff.html
|
||||
dihedral_style.html
|
||||
dimension.html
|
||||
displace_atoms.html
|
||||
dump.html
|
||||
|
|
@ -65,18 +57,12 @@ dump_netcdf.html
|
|||
dump_vtk.html
|
||||
dump_cfg_uef.html
|
||||
echo.html
|
||||
fix.html
|
||||
fix_modify.html
|
||||
group.html
|
||||
group2ndx.html
|
||||
if.html
|
||||
improper_coeff.html
|
||||
improper_style.html
|
||||
include.html
|
||||
info.html
|
||||
jump.html
|
||||
kspace_modify.html
|
||||
kspace_style.html
|
||||
label.html
|
||||
lattice.html
|
||||
log.html
|
||||
|
|
@ -91,10 +77,6 @@ neighbor.html
|
|||
newton.html
|
||||
next.html
|
||||
package.html
|
||||
pair_coeff.html
|
||||
pair_modify.html
|
||||
pair_style.html
|
||||
pair_write.html
|
||||
partition.html
|
||||
prd.html
|
||||
print.html
|
||||
|
|
@ -135,6 +117,9 @@ write_data.html
|
|||
write_dump.html
|
||||
write_restart.html
|
||||
|
||||
lammps_commands_fix.html
|
||||
fix.html
|
||||
fix_modify.html
|
||||
fix_adapt.html
|
||||
fix_adapt_fep.html
|
||||
fix_addforce.html
|
||||
|
|
@ -300,6 +285,9 @@ fix_wall_reflect.html
|
|||
fix_wall_region.html
|
||||
fix_wall_srd.html
|
||||
|
||||
lammps_commands_compute.html
|
||||
compute.html
|
||||
compute_modify.html
|
||||
compute_ackland_atom.html
|
||||
compute_angle.html
|
||||
compute_angle_local.html
|
||||
|
|
@ -418,6 +406,11 @@ compute_vcm_chunk.html
|
|||
compute_voronoi_atom.html
|
||||
compute_xrd.html
|
||||
|
||||
lammps_commands_pair.html
|
||||
pair_style.html
|
||||
pair_coeff.html
|
||||
pair_modify.html
|
||||
pair_write.html
|
||||
pair_adp.html
|
||||
pair_agni.html
|
||||
pair_airebo.html
|
||||
|
|
@ -523,6 +516,10 @@ pair_yukawa_colloid.html
|
|||
pair_zbl.html
|
||||
pair_zero.html
|
||||
|
||||
lammps_commands_bond.html
|
||||
bond_style.html
|
||||
bond_coeff.html
|
||||
bond_write.html
|
||||
bond_class2.html
|
||||
bond_fene.html
|
||||
bond_fene_expand.html
|
||||
|
|
@ -539,6 +536,9 @@ bond_quartic.html
|
|||
bond_table.html
|
||||
bond_zero.html
|
||||
|
||||
lammps_commands_angle.html
|
||||
angle_style.html
|
||||
angle_coeff.html
|
||||
angle_charmm.html
|
||||
angle_class2.html
|
||||
angle_cosine.html
|
||||
|
|
@ -559,6 +559,9 @@ angle_sdk.html
|
|||
angle_table.html
|
||||
angle_zero.html
|
||||
|
||||
lammps_commands_dihedral.html
|
||||
dihedral_style.html
|
||||
dihedral_coeff.html
|
||||
dihedral_charmm.html
|
||||
dihedral_class2.html
|
||||
dihedral_cosine_shift_exp.html
|
||||
|
|
@ -575,6 +578,9 @@ dihedral_spherical.html
|
|||
dihedral_table.html
|
||||
dihedral_zero.html
|
||||
|
||||
lammps_commands_improper.html
|
||||
improper_style.html
|
||||
improper_coeff.html
|
||||
improper_class2.html
|
||||
improper_cossq.html
|
||||
improper_cvff.html
|
||||
|
|
@ -588,6 +594,11 @@ improper_ring.html
|
|||
improper_umbrella.html
|
||||
improper_zero.html
|
||||
|
||||
lammps_commands_kspace.html
|
||||
kspace_style.html
|
||||
kspace_modify.html
|
||||
|
||||
lammps_commands_atc.html
|
||||
fix_atc.html
|
||||
USER/atc/man_add_molecule.html
|
||||
USER/atc/man_add_species.html
|
||||
|
|
|
|||
|
|
@ -8,3 +8,5 @@ command categories like compute styles or pair styles and so on.
|
|||
|
||||
The documentation for the USER-ATC package fix_modify commands
|
||||
follow at the very end of this manual.
|
||||
|
||||
General Commands :h2
|
||||
|
|
|
|||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Angle Style Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
AtC Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Bond Style Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Compute Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Dihedral Style Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Fix Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Improper Style Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Kspace Style Commands :h2
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
|
||||
Pair Style Commands :h2
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
|
||||
Supporting Information :h1
|
||||
|
||||
This section of the manual contains supporting information that
|
||||
is not documenting individual commands but general concepts and
|
||||
supporting information about entities like body particles or
|
||||
manifolds.
|
||||
|
|
@ -6,7 +6,7 @@
|
|||
|
||||
:line
|
||||
|
||||
Manifolds (surfaces) :h1
|
||||
Manifolds (surfaces) :h2
|
||||
|
||||
[Overview:]
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue