(a8cf1de7) · Commits · 郑智淋 / lammps

doc/Developers.pdf→doc/Developer.pdf

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doc/Manual.txt

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		@@ -40,7 +40,7 @@ The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
		about once per month. This is because it is large, and we don't want
		it to be part of very patch. :l

		There is also a "Developers.pdf"_Developers.pdf file in the doc
		There is also a "Developer.pdf"_Developer.pdf file in the doc
		directory, which describes the internal structure and algorithms of
		LAMMPS. :ule,l

doc/Section_accelerate.html

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		@@ -58,9 +58,9 @@ The speed-up due to GPU usage depends on a variety of factors, as
		discussed below.
		</P>
		<P>To see what styles are currently available in each of the accelerated
		packages, see <A HREF = "Section_commands.html#3_5">this section</A> of the manual.
		A list of accelerated styles is included in the pair, fix, compute,
		and kspace sections.
		packages, see <A HREF = "Section_commands.html#cmd_5">this section</A> of the
		manual. A list of accelerated styles is included in the pair, fix,
		compute, and kspace sections.
		</P>
		<P>The following sections explain:
		</P>
		@@ -73,17 +73,17 @@ 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 = "#5_1">OPT package</A><BR>
		5.2 <A HREF = "#5_2">USER-OMP package</A><BR>
		5.3 <A HREF = "#5_3">GPU package</A><BR>
		5.4 <A HREF = "#5_4">USER-CUDA package</A><BR>
		5.5 <A HREF = "#5_4">Comparison of GPU and USER-CUDA packages</A> <BR>
		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>

		<H4><A NAME = "5_1"></A>5.1 OPT package
		<H4><A NAME = "acc_1"></A>5.1 OPT package
		</H4>
		<P>The OPT package was developed by James Fischer (High Performance
		Technologies), David Richie, and Vincent Natoli (Stone Ridge
		@@ -112,7 +112,7 @@ to 20% savings.

		<HR>

		<H4><A NAME = "5_2"></A>5.2 USER-OMP package
		<H4><A NAME = "acc_2"></A>5.2 USER-OMP package
		</H4>
		<P>This section will be written when the USER-OMP package is released
		in main LAMMPS.
		@@ -121,7 +121,7 @@ in main LAMMPS.

		<HR>

		<H4><A NAME = "5_3"></A>5.3 GPU package
		<H4><A NAME = "acc_3"></A>5.3 GPU package
		</H4>
		<P>The GPU package was developed by Mike Brown at ORNL. It provides GPU
		versions of several pair styles and for long-range Coulombics via the
		@@ -263,7 +263,7 @@ requires that your GPU card support double precision.

		<HR>

		<H4><A NAME = "5_4"></A>5.4 USER-CUDA package
		<H4><A NAME = "acc_4"></A>5.4 USER-CUDA package
		</H4>
		<P>The USER-CUDA package was developed by Christian Trott at U Technology
		Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
		@@ -396,7 +396,7 @@ occurs, the faster your simulation will run.

		<HR>

		<H4><A NAME = "5_5"></A>5.5 Comparison of GPU and USER-CUDA packages
		<H4><A NAME = "acc_5"></A>5.5 Comparison of GPU and USER-CUDA packages
		</H4>
		<P>Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
		using NVIDIA hardware, but they do it in different ways.

doc/Section_accelerate.txt

+13 −13

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		@@ -55,9 +55,9 @@ The speed-up due to GPU usage depends on a variety of factors, as
		discussed below.

		To see what styles are currently available in each of the accelerated
		packages, see "this section"_Section_commands.html#3_5 of the manual.
		A list of accelerated styles is included in the pair, fix, compute,
		and kspace sections.
		packages, see "this section"_Section_commands.html#cmd_5 of the
		manual. A list of accelerated styles is included in the pair, fix,
		compute, and kspace sections.

		The following sections explain:

		@@ -70,16 +70,16 @@ 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"_#5_1
		5.2 "USER-OMP package"_#5_2
		5.3 "GPU package"_#5_3
		5.4 "USER-CUDA package"_#5_4
		5.5 "Comparison of GPU and USER-CUDA packages"_#5_4 :all(b)
		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

		5.1 OPT package :h4,link(5_1)
		5.1 OPT package :h4,link(acc_1)

		The OPT package was developed by James Fischer (High Performance
		Technologies), David Richie, and Vincent Natoli (Stone Ridge
		@@ -107,7 +107,7 @@ to 20% savings.
		:line
		:line

		5.2 USER-OMP package :h4,link(5_2)
		5.2 USER-OMP package :h4,link(acc_2)

		This section will be written when the USER-OMP package is released
		in main LAMMPS.
		@@ -115,7 +115,7 @@ in main LAMMPS.
		:line
		:line

		5.3 GPU package :h4,link(5_3)
		5.3 GPU package :h4,link(acc_3)

		The GPU package was developed by Mike Brown at ORNL. It provides GPU
		versions of several pair styles and for long-range Coulombics via the
		@@ -256,7 +256,7 @@ requires that your GPU card support double precision.
		:line
		:line

		5.4 USER-CUDA package :h4,link(5_4)
		5.4 USER-CUDA package :h4,link(acc_4)

		The USER-CUDA package was developed by Christian Trott at U Technology
		Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
		@@ -388,7 +388,7 @@ occurs, the faster your simulation will run.
		:line
		:line

		5.5 Comparison of GPU and USER-CUDA packages :h4,link(5_5)
		5.5 Comparison of GPU and USER-CUDA packages :h4,link(acc_5)

		Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
		using NVIDIA hardware, but they do it in different ways.

doc/Section_commands.html

+15 −15

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		@@ -14,15 +14,15 @@
		<P>This section describes how a LAMMPS input script is formatted and what
		commands are used to define a LAMMPS simulation.
		</P>
		3.1 <A HREF = "#3_1">LAMMPS input script</A><BR>
		3.2 <A HREF = "#3_2">Parsing rules</A><BR>
		3.3 <A HREF = "#3_3">Input script structure</A><BR>
		3.4 <A HREF = "#3_4">Commands listed by category</A><BR>
		3.5 <A HREF = "#3_5">Commands listed alphabetically</A> <BR>
		3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
		3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
		3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
		3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
		3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>

		<HR>

		<A NAME = "3_1"></A><H4>3.1 LAMMPS input script
		<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
		</H4>
		<P>LAMMPS executes by reading commands from a input script (text file),
		one line at a time. When the input script ends, LAMMPS exits. Each
		@@ -75,7 +75,7 @@ command lists restrictions on how the command can be used.
		</P>
		<HR>

		<A NAME = "3_2"></A><H4>3.2 Parsing rules
		<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
		</H4>
		<P>Each non-blank line in the input script is treated as a command.
		LAMMPS commands are case sensitive. Command names are lower-case, as
		@@ -134,7 +134,7 @@ allowed, but that should be sufficient for most use cases.
		</P>
		<HR>

		<H4><A NAME = "3_3"></A>3.3 Input script structure
		<H4><A NAME = "cmd_3"></A>3.3 Input script structure
		</H4>
		<P>This section describes the structure of a typical LAMMPS input script.
		The "examples" directory in the LAMMPS distribution contains many
		@@ -223,11 +223,11 @@ the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
		</P>
		<HR>

		<A NAME = "3_4"></A><H4>3.4 Commands listed by category
		<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
		</H4>
		<P>This section lists all LAMMPS commands, grouped by category. The
		<A HREF = "#3_5">next section</A> lists the same commands alphabetically. Note that
		some style options for some commands are part of specific LAMMPS
		<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
		that some style options for some commands are part of specific LAMMPS
		packages, which means they cannot be used unless the package was
		included when LAMMPS was built. Not all packages are included in a
		default LAMMPS build. These dependencies are listed as Restrictions
		@@ -300,12 +300,12 @@ in the command's documentation.
		</P>
		<HR>

		<H4><A NAME = "3_5"></A><A NAME = "comm"></A>3.5 Individual commands
		<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
		</H4>
		<P>This section lists all LAMMPS commands alphabetically, with a separate
		listing below of styles within certain commands. The <A HREF = "#3_4">previous
		section</A> lists the same commands, grouped by category. Note that
		some style options for some commands are part of specific LAMMPS
		listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
		section</A> lists the same commands, grouped by category. Note
		that some style options for some commands are part of specific LAMMPS
		packages, which means they cannot be used unless the package was
		included when LAMMPS was built. Not all packages are included in a
		default LAMMPS build. These dependencies are listed as Restrictions

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