Merge pull request #846 from akohlmey/pdf-manual-reorg

endif

SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')

SOURCES=$(filter-out src/lammps_commands.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))

SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))

OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)

.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check

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<H1></H1>

LAMMPS Documentation :c,h1

16 Mar 2018 version :c,h2

LAMMPS Documentation :c,h3

16 Mar 2018 version :c,h4

Version info: :h4

Version info: :h3

The LAMMPS "version" is the date when it was released, such as 1 May

2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a

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5. Accelerating LAMMPS performance :h3

5. Accelerating LAMMPS performance :h2

This section describes various methods for improving LAMMPS

performance for different classes of problems running on different

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5.1 Measuring performance :h4,link(acc_1)

5.1 Measuring performance :h3,link(acc_1)

Before trying to make your simulation run faster, you should

understand how it currently performs and where the bottlenecks are.

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5.2 General strategies :h4,link(acc_2)

5.2 General strategies :h3,link(acc_2)

NOTE: this section 5.2 is still a work in progress

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5.3 Packages with optimized styles :h4,link(acc_3)

5.3 Packages with optimized styles :h3,link(acc_3)

Accelerated versions of various "pair_style"_pair_style.html,

"fixes"_fix.html, "computes"_compute.html, and other commands have

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5.4 Comparison of various accelerator packages :h4,link(acc_4)

5.4 Comparison of various accelerator packages :h3,link(acc_4)

NOTE: this section still needs to be re-worked with additional KOKKOS

and USER-INTEL information.

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3. Commands :h3

3. Commands :h2

This section describes how a LAMMPS input script is formatted and the

input script commands used to define a LAMMPS simulation.

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3.3 Input script structure :h4,link(cmd_3)

3.3 Input script structure :h3,link(cmd_3)

This section describes the structure of a typical LAMMPS input script.

The "examples" directory in the LAMMPS distribution contains many

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3.5 Individual commands :h4,link(cmd_5),link(comm)

3.5 Individual commands :h3,link(cmd_5),link(comm)

This section lists all LAMMPS commands alphabetically, with a separate

listing below of styles within certain commands.  The "previous

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Fix styles :h4

Fix styles :h3

See the "fix"_fix.html command for one-line descriptions of each style

or click on the style itself for a full description.  Some of the

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Compute styles :h4

Compute styles :h3

See the "compute"_compute.html command for one-line descriptions of

each style or click on the style itself for a full description.  Some

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Pair_style potentials :h4

Pair_style potentials :h3

See the "pair_style"_pair_style.html command for an overview of pair

potentials.  Click on the style itself for a full description.  Many

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Bond_style potentials :h4

Bond_style potentials :h3

See the "bond_style"_bond_style.html command for an overview of bond

potentials.  Click on the style itself for a full description.  Some

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Angle_style potentials :h4

Angle_style potentials :h3

See the "angle_style"_angle_style.html command for an overview of

angle potentials.  Click on the style itself for a full description.

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Dihedral_style potentials :h4

Dihedral_style potentials :h3

See the "dihedral_style"_dihedral_style.html command for an overview

of dihedral potentials.  Click on the style itself for a full

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Improper_style potentials :h4

Improper_style potentials :h3

See the "improper_style"_improper_style.html command for an overview

of improper potentials.  Click on the style itself for a full

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Kspace solvers :h4

Kspace solvers :h3

See the "kspace_style"_kspace_style.html command for an overview of

Kspace solvers.  Click on the style itself for a full description.

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12. Errors :h3

12. Errors :h2

This section describes the errors you can encounter when using LAMMPS,

either conceptually, or as printed out by the program.

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12.3 Error & warning messages :h4,link(err_3)

12.3 Error & warning messages :h3,link(err_3)

These are two alphabetic lists of the "ERROR"_#error and

"WARNING"_#warn messages LAMMPS prints out and the reason why.  If the

error occurs and is not self-explanatory, you'll need to look in the

source code or contact the author of the package.

Errors: :h4,link(error)

Errors: :h3,link(error)

:dlb

:dle

Warnings: :h4,link(warn)

Warnings: :h3,link(warn)

:dlb