Commit d0d785e3 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6807 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent b5a3443d

doc/Manual.html

+110 −40
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@@ -122,49 +122,67 @@ it gives quick access to documentation for all LAMMPS commands. 
<BR>

  3.5 <A HREF = "Section_commands.html#3_5">Commands listed alphabetically</A> 

<BR></UL>

<LI><A HREF = "Section_packages.html">Packages</A> 



<UL>  4.1 <A HREF = "Section_commands.html#3_1">Standard packages</A> 

<BR>

  4.2 <A HREF = "Section_commands.html#3_2">User packages</A> 

<BR></UL>

<LI><A HREF = "Section_accelerate.html">Using accelerated CPU and GPU styles</A> 



<UL>  5.1 <A HREF = "Section_howto.html#4_1">OPT package</A> 

<BR>

  5.2 <A HREF = "Section_howto.html#4_2">USER-OMP package</A> 

<BR>

  5.3 <A HREF = "Section_howto.html#4_3">GPU package</A> 

<BR>

  5.4 <A HREF = "Section_howto.html#4_4">USER-CUDA package</A> 

<BR>

  5.5 <A HREF = "Section_howto.html#4_5">Comparison of GPU and USER-CUDA packages</A> 

<BR></UL>

<LI><A HREF = "Section_howto.html">How-to discussions</A> 



<UL>  4.1 <A HREF = "Section_howto.html#4_1">Restarting a simulation</A> 

<UL>  6.1 <A HREF = "Section_commands.html#4_1">Restarting a simulation</A> 

<BR>

  4.2 <A HREF = "Section_howto.html#4_2">2d simulations</A> 

  6.2 <A HREF = "Section_commands.html#4_2">2d simulations</A> 

<BR>

  4.3 <A HREF = "Section_howto.html#4_3">CHARMM and AMBER force fields</A> 

  6.3 <A HREF = "4_3">CHARMM and AMBER force fields</A> 

<BR>

  4.4 <A HREF = "Section_howto.html#4_4">Running multiple simulations from one input script</A> 

  6.4 <A HREF = "4_4">Running multiple simulations from one input script</A> 

<BR>

  4.5 <A HREF = "Section_howto.html#4_5">Multi-replica simulations</A> 

  6.5 <A HREF = "4_5">Multi-replica simulations</A> 

<BR>

  4.6 <A HREF = "Section_howto.html#4_6">Granular models</A> 

  6.6 <A HREF = "4_6">Granular models</A> 

<BR>

  4.7 <A HREF = "Section_howto.html#4_7">TIP3P water model</A> 

  6.7 <A HREF = "4_7">TIP3P water model</A> 

<BR>

  4.8 <A HREF = "Section_howto.html#4_8">TIP4P water model</A> 

  6.8 <A HREF = "4_8">TIP4P water model</A> 

<BR>

  4.9 <A HREF = "Section_howto.html#4_9">SPC water model</A> 

  6.9 <A HREF = "4_9">SPC water model</A> 

<BR>

  4.10 <A HREF = "Section_howto.html#4_10">Coupling LAMMPS to other codes</A> 

  6.10 <A HREF = "4_10">Coupling LAMMPS to other codes</A> 

<BR>

  4.11 <A HREF = "Section_howto.html#4_11">Visualizing LAMMPS snapshots</A> 

  6.11 <A HREF = "4_11">Visualizing LAMMPS snapshots</A> 

<BR>

  4.12 <A HREF = "Section_howto.html#4_12">Triclinic (non-orthogonal) simulation boxes</A> 

  6.12 <A HREF = "4_12">Triclinic (non-orthogonal) simulation boxes</A> 

<BR>

  4.13 <A HREF = "Section_howto.html#4_13">NEMD simulations</A> 

  6.13 <A HREF = "4_13">NEMD simulations</A> 

<BR>

  4.14 <A HREF = "Section_howto.html#4_14">Extended spherical and aspherical particles</A> 

  6.14 <A HREF = "4_14">Extended spherical and aspherical particles</A> 

<BR>

  4.15 <A HREF = "Section_howto.html#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A> 

  6.15 <A HREF = "4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A> 

<BR>

  4.16 <A HREF = "Section_howto.html#4_16">Thermostatting, barostatting, and compute temperature</A> 

  6.16 <A HREF = "4_16">Thermostatting, barostatting, and compute temperature</A> 

<BR>

  4.17 <A HREF = "Section_howto.html#4_17">Walls</A> 

  6.17 <A HREF = "4_17">Walls</A> 

<BR>

  4.18 <A HREF = "Section_howto.html#4_18">Elastic constants</A> 

  6.18 <A HREF = "4_18">Elastic constants</A> 

<BR>

  4.19 <A HREF = "Section_howto.html#4_19">Library interface to LAMMPS</A> 

  6.19 <A HREF = "4_19">Library interface to LAMMPS</A> 

<BR>

  4.20 <A HREF = "Section_howto.html#4_20">Calculating thermal conductivity</A> 

  6.20 <A HREF = "4_20">Calculating thermal conductivity</A> 

<BR>

  4.21 <A HREF = "Section_howto.html#4_21">Calculating viscosity</A> 

  6.21 <A HREF = "4_21">Calculating viscosity</A> 

<BR></UL>

<LI><A HREF = "Section_example.html">Example problems</A>
@@ -174,45 +192,63 @@ it gives quick access to documentation for all LAMMPS commands. 


<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A> 



<LI><A HREF = "Section_python.html">Python interface</A> 



<UL>  9.1 <A HREF = "Section_python.html#9_1">Extending Python with a serial version of LAMMPS</A> 

<UL>  10.1 <A HREF = "Section_howto.html#4_1">Atom styles</A> 

<BR>

  10.2 <A HREF = "Section_howto.html#4_2">Bond, angle, dihedral, improper potentials</A> 

<BR>

  10.3 <A HREF = "Section_howto.html#4_3">Compute styles</A> 

<BR>

  10.4 <A HREF = "Section_howto.html#4_4">Dump styles</A> 

<BR>

  9.2 <A HREF = "Section_python.html#9_2">Creating a shared MPI library</A> 

  10.5 <A HREF = "Section_howto.html#4_5">Dump custom output options</A> 

<BR>

  9.3 <A HREF = "Section_python.html#9_3">Extending Python with a parallel version of LAMMPS</A> 

  10.6 <A HREF = "Section_howto.html#4_6">Fix styles</A> 

<BR>

  9.4 <A HREF = "Section_python.html#9_4">Extending Python with MPI</A> 

  10.7 <A HREF = "Section_howto.html#4_7">Input script commands</A> 

<BR>

  9.5 <A HREF = "Section_python.html#9_5">Testing the Python-LAMMPS interface</A> 

  10.8 <A HREF = "Section_howto.html#4_8">Kspace computations</A> 

<BR>

  9.6 <A HREF = "Section_python.html#9_6">Using LAMMPS from Python</A> 

  10.9 <A HREF = "Section_howto.html#4_9">Minimization styles</A> 

<BR>

  9.7 <A HREF = "Section_python.html#9_7">Example Python scripts that use LAMMPS</A> 

  10.10 <A HREF = "Section_howto.html#10_10">Pairwise potentials</A> 

<BR>

  10.11 <A HREF = "Section_howto.html#10_11">Region styles</A> 

<BR>

  10.12 <A HREF = "Section_howto.html#4_12">Thermodynamic output options</A> 

<BR>

  10.13 <A HREF = "Section_howto.html#4_13">Variable options</A> 

<BR>

  10.14 <A HREF = "Section_howto.html#4_14">Submitting new features for inclusion in LAMMPS</A> 

<BR></UL>

<LI><A HREF = "Section_accelerate.html">Using accelerated CPU and GPU styles</A> 

<LI><A HREF = "Section_python.html">Python interface</A> 



<UL>  10.1 <A HREF = "Section_accelerate.html#10_1">OPT package</A> 

<UL>  11.1 <A HREF = "9_1">Extending Python with a serial version of LAMMPS</A> 

<BR>

  11.2 <A HREF = "9_2">Creating a shared MPI library</A> 

<BR>

  10.2 <A HREF = "Section_accelerate.html#10_2">GPU package</A> 

  11.3 <A HREF = "9_3">Extending Python with a parallel version of LAMMPS</A> 

<BR>

  10.3 <A HREF = "Section_accelerate.html#10_3">USER-CUDA package</A> 

  11.4 <A HREF = "9_4">Extending Python with MPI</A> 

<BR>

  10.4 <A HREF = "Section_accelerate.html#10_4">Comparison of GPU and USER-CUDA packages</A> 

  11.5 <A HREF = "9_5">Testing the Python-LAMMPS interface</A> 

<BR>

  11.6 <A HREF = "9_6">Using LAMMPS from Python</A> 

<BR>

  11.7 <A HREF = "9_7">Example Python scripts that use LAMMPS</A> 

<BR></UL>

<LI><A HREF = "Section_errors.html">Errors</A> 



<UL>  11.1 <A HREF = "Section_errors.html#11_1">Common problems</A> 

<UL>  12.1 <A HREF = "Section_python.html#9_1">Common problems</A> 

<BR>

  11.2 <A HREF = "Section_errors.html#11_2">Reporting bugs</A> 

  12.2 <A HREF = "Section_python.html#9_2">Reporting bugs</A> 

<BR>

  11.3 <A HREF = "Section_errors.html#11_3">Error & warning messages</A> 

  12.3 <A HREF = "Section_python.html#9_3">Error & warning messages</A> 

<BR></UL>

<LI><A HREF = "Section_history.html">Future and history</A> 



<UL>  12.1 <A HREF = "Section_history.html#12_1">Coming attractions</A> 

<UL>  13.1 <A HREF = "Section_errors.html#11_1">Coming attractions</A> 

<BR>

  12.2 <A HREF = "Section_history.html#12_2">Past versions</A> 

  13.2 <A HREF = "Section_errors.html#11_2">Past versions</A> 

<BR></UL>



</OL>
@@ -305,6 +341,40 @@ it gives quick access to documentation for all LAMMPS commands.

doc/Manual.txt

+116 −79
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@@ -97,52 +97,70 @@ it gives quick access to documentation for all LAMMPS commands. 
  3.3 "Input script structure"_3_3 :b

  3.4 "Commands listed by category"_3_4 :b

  3.5 "Commands listed alphabetically"_3_5 :ule,b

"Packages"_Section_packages.html :l

  4.1 "Standard packages"_3_1 :ulb,b

  4.2 "User packages"_3_2 :ule,b

"Using accelerated CPU and GPU styles"_Section_accelerate.html :l

  5.1 "OPT package"_10_1 :ulb,b

  5.2 "USER-OMP package"_10_2 :b

  5.3 "GPU package"_10_3 :b

  5.4 "USER-CUDA package"_10_4 :b

  5.5 "Comparison of GPU and USER-CUDA packages"_10_5 :ule,b

"How-to discussions"_Section_howto.html :l

  4.1 "Restarting a simulation"_4_1 :ulb,b

  4.2 "2d simulations"_4_2 :b

  4.3 "CHARMM and AMBER force fields"_4_3 :b

  4.4 "Running multiple simulations from one input script"_4_4 :b

  4.5 "Multi-replica simulations"_4_5 :b

  4.6 "Granular models"_4_6 :b

  4.7 "TIP3P water model"_4_7 :b

  4.8 "TIP4P water model"_4_8 :b

  4.9 "SPC water model"_4_9 :b

  4.10 "Coupling LAMMPS to other codes"_4_10 :b

  4.11 "Visualizing LAMMPS snapshots"_4_11 :b

  4.12 "Triclinic (non-orthogonal) simulation boxes"_4_12 :b

  4.13 "NEMD simulations"_4_13 :b

  4.14 "Extended spherical and aspherical particles"_4_14 :b

  4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_4_15 :b

  4.16 "Thermostatting, barostatting, and compute temperature"_4_16 :b

  4.17 "Walls"_4_17 :b

  4.18 "Elastic constants"_4_18 :b

  4.19 "Library interface to LAMMPS"_4_19 :b

  4.20 "Calculating thermal conductivity"_4_20 :b

  4.21 "Calculating viscosity"_4_21 :ule,b

  6.1 "Restarting a simulation"_4_1 :ulb,b

  6.2 "2d simulations"_4_2 :b

  6.3 "CHARMM and AMBER force fields"_4_3 :b

  6.4 "Running multiple simulations from one input script"_4_4 :b

  6.5 "Multi-replica simulations"_4_5 :b

  6.6 "Granular models"_4_6 :b

  6.7 "TIP3P water model"_4_7 :b

  6.8 "TIP4P water model"_4_8 :b

  6.9 "SPC water model"_4_9 :b

  6.10 "Coupling LAMMPS to other codes"_4_10 :b

  6.11 "Visualizing LAMMPS snapshots"_4_11 :b

  6.12 "Triclinic (non-orthogonal) simulation boxes"_4_12 :b

  6.13 "NEMD simulations"_4_13 :b

  6.14 "Extended spherical and aspherical particles"_4_14 :b

  6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_4_15 :b

  6.16 "Thermostatting, barostatting, and compute temperature"_4_16 :b

  6.17 "Walls"_4_17 :b

  6.18 "Elastic constants"_4_18 :b

  6.19 "Library interface to LAMMPS"_4_19 :b

  6.20 "Calculating thermal conductivity"_4_20 :b

  6.21 "Calculating viscosity"_4_21 :ule,b

"Example problems"_Section_example.html :l

"Performance & scalability"_Section_perf.html :l

"Additional tools"_Section_tools.html :l

"Modifying & extending LAMMPS"_Section_modify.html :l

  10.1 "Atom styles"_10_1 :ulb,b

  10.2 "Bond, angle, dihedral, improper potentials"_10_2 :b

  10.3 "Compute styles"_10_3 :b

  10.4 "Dump styles"_10_4 :b

  10.5 "Dump custom output options"_10_5 :b

  10.6 "Fix styles"_10_6 :b

  10.7 "Input script commands"_10_7 :b

  10.8 "Kspace computations"_10_8 :b

  10.9 "Minimization styles"_10_9 :b

  10.10 "Pairwise potentials"_10_10 :b

  10.11 "Region styles"_10_11 :b

  10.12 "Thermodynamic output options"_10_12 :b

  10.13 "Variable options"_10_13 :b

  10.14 "Submitting new features for inclusion in LAMMPS"_10_14 :ule,b

"Python interface"_Section_python.html :l

  9.1 "Extending Python with a serial version of LAMMPS"_9_1 :ulb,b

  9.2 "Creating a shared MPI library"_9_2 :b

  9.3 "Extending Python with a parallel version of LAMMPS"_9_3 :b

  9.4 "Extending Python with MPI"_9_4 :b

  9.5 "Testing the Python-LAMMPS interface"_9_5 :b

  9.6 "Using LAMMPS from Python"_9_6 :b

  9.7 "Example Python scripts that use LAMMPS"_9_7 :ule,b

"Using accelerated CPU and GPU styles"_Section_accelerate.html :l

  10.1 "OPT package"_10_1 :ulb,b

  10.2 "GPU package"_10_2 :b

  10.3 "USER-CUDA package"_10_3 :b

  10.4 "Comparison of GPU and USER-CUDA packages"_10_4 :ule,b

  11.1 "Extending Python with a serial version of LAMMPS"_9_1 :ulb,b

  11.2 "Creating a shared MPI library"_9_2 :b

  11.3 "Extending Python with a parallel version of LAMMPS"_9_3 :b

  11.4 "Extending Python with MPI"_9_4 :b

  11.5 "Testing the Python-LAMMPS interface"_9_5 :b

  11.6 "Using LAMMPS from Python"_9_6 :b

  11.7 "Example Python scripts that use LAMMPS"_9_7 :ule,b

"Errors"_Section_errors.html :l

  11.1 "Common problems"_11_1 :ulb,b

  11.2 "Reporting bugs"_11_2 :b

  11.3 "Error & warning messages"_11_3 :ule,b

  12.1 "Common problems"_11_1 :ulb,b

  12.2 "Reporting bugs"_11_2 :b

  12.3 "Error & warning messages"_11_3 :ule,b

"Future and history"_Section_history.html :l

  12.1 "Coming attractions"_12_1 :ulb,b

  12.2 "Past versions"_12_2 :ule,b

  13.1 "Coming attractions"_12_1 :ulb,b

  13.2 "Past versions"_12_2 :ule,b

:ole



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doc/Section_accelerate.html

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<HTML>

<CENTER><A HREF = "Section_python.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -

<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_errors.html">Next

<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -

<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next

Section</A> 

</CENTER>
@@ -11,7 +11,7 @@ Section</A> 


<HR>



<H3>10. Using accelerated CPU and GPU styles 

<H3>5. Using accelerated CPU and GPU styles 

</H3>

<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,

<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
@@ -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>

10.1 <A HREF = "#10_1">OPT package</A><BR>

10.2 <A HREF = "#10_2">USER-OMP package</A><BR>

10.3 <A HREF = "#10_3">GPU package</A><BR>

10.4 <A HREF = "#10_4">USER-CUDA package</A><BR>

10.5 <A HREF = "#10_4">Comparison of GPU and USER-CUDA packages</A> <BR>

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>



<HR>



<HR>



<H4><A NAME = "10_1"></A>10.1 OPT package 

<H4><A NAME = "5_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 = "10_2"></A>10.2 USER-OMP package 

<H4><A NAME = "5_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 = "10_3"></A>10.3 GPU package 

<H4><A NAME = "5_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 = "10_4"></A>10.4 USER-CUDA package 

<H4><A NAME = "5_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 = "10_5"></A>10.5 Comparison of GPU and USER-CUDA packages 

<H4><A NAME = "5_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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"Previous Section"_Section_python.html - "LAMMPS WWW Site"_lws -

"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -

"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next

Section"_Section_errors.html :c

Section"_Section_howto.html :c



:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)
@@ -8,7 +8,7 @@ Section"_Section_errors.html :c 


:line



10. Using accelerated CPU and GPU styles :h3

5. Using accelerated CPU and GPU styles :h3



Accelerated versions of various "pair_style"_pair_style.html,

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



10.1 "OPT package"_#10_1

10.2 "USER-OMP package"_#10_2

10.3 "GPU package"_#10_3

10.4 "USER-CUDA package"_#10_4

10.5 "Comparison of GPU and USER-CUDA packages"_#10_4 :all(b)

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)



:line

:line



10.1 OPT package :h4,link(10_1)

5.1 OPT package :h4,link(5_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



10.2 USER-OMP package :h4,link(10_2)

5.2 USER-OMP package :h4,link(5_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



10.3 GPU package :h4,link(10_3)

5.3 GPU package :h4,link(5_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



10.4 USER-CUDA package :h4,link(10_4)

5.4 USER-CUDA package :h4,link(5_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



10.5 Comparison of GPU and USER-CUDA packages :h4,link(10_5)

5.5 Comparison of GPU and USER-CUDA packages :h4,link(5_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

+1 −1
Original line number Diff line number Diff line 
<HTML>

<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next Section</A> 

<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A> 

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