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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>
<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>
10.5 <A HREF = "Section_howto.html#4_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_howto.html#4_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_howto.html#4_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_howto.html#4_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_howto.html#4_9">Minimization styles</A>
<BR>
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_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> 11.1 <A HREF = "9_1">Extending Python with a serial version of LAMMPS</A>
<BR>
9.2 <A HREF = "Section_python.html#9_2">Creating a shared MPI library</A>
11.2 <A HREF = "9_2">Creating a shared MPI library</A>
<BR>
9.3 <A HREF = "Section_python.html#9_3">Extending Python with a parallel version of LAMMPS</A>
11.3 <A HREF = "9_3">Extending Python with a parallel version of LAMMPS</A>
<BR>
9.4 <A HREF = "Section_python.html#9_4">Extending Python with MPI</A>
11.4 <A HREF = "9_4">Extending Python with MPI</A>
<BR>
9.5 <A HREF = "Section_python.html#9_5">Testing the Python-LAMMPS interface</A>
11.5 <A HREF = "9_5">Testing the Python-LAMMPS interface</A>
<BR>
9.6 <A HREF = "Section_python.html#9_6">Using LAMMPS from Python</A>
11.6 <A HREF = "9_6">Using LAMMPS from Python</A>
<BR>
9.7 <A HREF = "Section_python.html#9_7">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Using accelerated CPU and GPU styles</A>
<UL> 10.1 <A HREF = "Section_accelerate.html#10_1">OPT package</A>
<BR>
10.2 <A HREF = "Section_accelerate.html#10_2">GPU package</A>
<BR>
10.3 <A HREF = "Section_accelerate.html#10_3">USER-CUDA package</A>
<BR>
10.4 <A HREF = "Section_accelerate.html#10_4">Comparison of GPU and USER-CUDA packages</A>
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.

187
doc/Manual.txt
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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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@ -166,46 +184,65 @@ it gives quick access to documentation for all LAMMPS commands.
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@ -1,6 +1,6 @@
<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.

26
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@ -1,6 +1,6 @@
"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.

2
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@ -1,5 +1,5 @@
<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>
</CENTER>

2
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@ -1,4 +1,4 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_howto.html :c
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)

16
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@ -11,18 +11,18 @@ Section</A>
<HR>
<H3>11. Errors
<H3>12. Errors
</H3>
<P>This section describes the various kinds of errors you can encounter
when using LAMMPS.
</P>
11.1 <A HREF = "#11_1">Common problems</A><BR>
11.2 <A HREF = "#11_2">Reporting bugs</A><BR>
11.3 <A HREF = "#11_3">Error & warning messages</A> <BR>
12.1 <A HREF = "#12_1">Common problems</A><BR>
12.2 <A HREF = "#12_2">Reporting bugs</A><BR>
12.3 <A HREF = "#12_3">Error & warning messages</A> <BR>
<HR>
<A NAME = "11_1"></A><H4>11.1 Common problems
<A NAME = "12_1"></A><H4>12.1 Common problems
</H4>
<P>If two LAMMPS runs do not produce the same answer on different
machines or different numbers of processors, this is typically not a
@ -81,7 +81,7 @@ decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
could be a bug (see <A HREF = "#11_2">this section</A>) or one of the following
could be a bug (see <A HREF = "#12_2">this section</A>) or one of the following
cases:
</P>
<P>LAMMPS runs in the available memory a processor allows to be
@ -112,7 +112,7 @@ buffering or boost the sizes of messages that can be buffered.
</P>
<HR>
<A NAME = "11_2"></A><H4>11.2 Reporting bugs
<A NAME = "12_2"></A><H4>12.2 Reporting bugs
</H4>
<P>If you are confident that you have found a bug in LAMMPS, follow these
steps.
@ -142,7 +142,7 @@ causing the problem.
</P>
<HR>
<H4><A NAME = "11_3"></A>11.3 Error & warning messages
<H4><A NAME = "12_3"></A>12.3 Error & warning messages
</H4>
<P>These are two alphabetic lists of the <A HREF = "#error">ERROR</A> and
<A HREF = "#warn">WARNING</A> messages LAMMPS prints out and the reason why. If the

16
doc/Section_errors.txt
View File

@ -8,18 +8,18 @@ Section"_Section_history.html :c
:line
11. Errors :h3
12. Errors :h3
This section describes the various kinds of errors you can encounter
when using LAMMPS.
11.1 "Common problems"_#11_1
11.2 "Reporting bugs"_#11_2
11.3 "Error & warning messages"_#11_3 :all(b)
12.1 "Common problems"_#12_1
12.2 "Reporting bugs"_#12_2
12.3 "Error & warning messages"_#12_3 :all(b)
:line
11.1 Common problems :link(11_1),h4
12.1 Common problems :link(12_1),h4
If two LAMMPS runs do not produce the same answer on different
machines or different numbers of processors, this is typically not a
@ -78,7 +78,7 @@ decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
could be a bug (see "this section"_#11_2) or one of the following
could be a bug (see "this section"_#12_2) or one of the following
cases:
LAMMPS runs in the available memory a processor allows to be
@ -109,7 +109,7 @@ buffering or boost the sizes of messages that can be buffered.
:line
11.2 Reporting bugs :link(11_2),h4
12.2 Reporting bugs :link(12_2),h4
If you are confident that you have found a bug in LAMMPS, follow these
steps.
@ -139,7 +139,7 @@ As a last resort, you can send an email directly to the
:line
11.3 Error & warning messages :h4,link(11_3)
12.3 Error & warning messages :h4,link(12_3)
These are two alphabetic lists of the "ERROR"_#error and
"WARNING"_#warn messages LAMMPS prints out and the reason why. If the

2
doc/Section_example.html
View File

@ -9,7 +9,7 @@
<HR>
<H3>5. Example problems
<H3>7. Example problems
</H3>
<P>The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its

2
doc/Section_example.txt
View File

@ -6,7 +6,7 @@
:line
5. Example problems :h3
7. Example problems :h3
The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its

10
doc/Section_history.html
View File

@ -9,18 +9,18 @@
<HR>
<H3>12. Future and history
<H3>13. Future and history
</H3>
<P>This section lists features we are planning to add to LAMMPS, features
of previous versions of LAMMPS, and features of other parallel
molecular dynamics codes I've distributed.
</P>
12.1 <A HREF = "#12_1">Coming attractions</A><BR>
12.2 <A HREF = "#12_2">Past versions</A> <BR>
13.1 <A HREF = "#13_1">Coming attractions</A><BR>
13.2 <A HREF = "#13_2">Past versions</A> <BR>
<HR>
<H4><A NAME = "12_1"></A>12.1 Coming attractions
<H4><A NAME = "13_1"></A>13.1 Coming attractions
</H4>
<P>The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes developed at Sandia. These include
@ -49,7 +49,7 @@ page</A> on the LAMMPS WWW site for more details.
</UL>
<HR>
<H4><A NAME = "12_2"></A>12.2 Past versions
<H4><A NAME = "13_2"></A>13.2 Past versions
</H4>
<P>LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)

10
doc/Section_history.txt
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@ -6,18 +6,18 @@
:line
12. Future and history :h3
13. Future and history :h3
This section lists features we are planning to add to LAMMPS, features
of previous versions of LAMMPS, and features of other parallel
molecular dynamics codes I've distributed.
12.1 "Coming attractions"_#12_1
12.2 "Past versions"_#12_2 :all(b)
13.1 "Coming attractions"_#13_1
13.2 "Past versions"_#13_2 :all(b)
:line
12.1 Coming attractions :h4,link(12_1)
13.1 Coming attractions :h4,link(13_1)
The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes developed at Sandia. These include
@ -46,7 +46,7 @@ Direct Simulation Monte Carlo - DSMC :ul
:line
12.2 Past versions :h4,link(12_2)
13.2 Past versions :h4,link(13_2)
LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)

104
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@ -1,5 +1,5 @@
<HTML>
<CENTER><A HREF = "Section_commands.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_example.html">Next Section</A>
<CENTER><A HREF = "Section_accelerate.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_example.html">Next Section</A>
</CENTER>
@ -9,32 +9,32 @@
<HR>
<H3>4. How-to discussions
<H3>6. How-to discussions
</H3>
<P>The following sections describe how to use various options within
LAMMPS.
</P>
4.1 <A HREF = "#4_1">Restarting a simulation</A><BR>
4.2 <A HREF = "#4_2">2d simulations</A><BR>
4.3 <A HREF = "#4_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
4.4 <A HREF = "#4_4">Running multiple simulations from one input script</A><BR>
4.5 <A HREF = "#4_5">Multi-replica simulations</A><BR>
4.6 <A HREF = "#4_6">Granular models</A><BR>
4.7 <A HREF = "#4_7">TIP3P water model</A><BR>
4.8 <A HREF = "#4_8">TIP4P water model</A><BR>
4.9 <A HREF = "#4_9">SPC water model</A><BR>
4.10 <A HREF = "#4_10">Coupling LAMMPS to other codes</A><BR>
4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A><BR>
4.12 <A HREF = "#4_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
4.14 <A HREF = "#4_14">Extended spherical and aspherical particles</A><BR>
4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A><BR>
4.17 <A HREF = "#4_17">Walls</A><BR>
4.18 <A HREF = "#4_18">Elastic constants</A><BR>
4.19 <A HREF = "#4_19">Library interface to LAMMPS</A><BR>
4.20 <A HREF = "#4_20">Calculating thermal conductivity</A><BR>
4.21 <A HREF = "#4_21">Calculating viscosity</A> <BR>
6.1 <A HREF = "#6_1">Restarting a simulation</A><BR>
6.2 <A HREF = "#6_2">2d simulations</A><BR>
6.3 <A HREF = "#6_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
6.4 <A HREF = "#6_4">Running multiple simulations from one input script</A><BR>
6.5 <A HREF = "#6_5">Multi-replica simulations</A><BR>
6.6 <A HREF = "#6_6">Granular models</A><BR>
6.7 <A HREF = "#6_7">TIP3P water model</A><BR>
6.8 <A HREF = "#6_8">TIP4P water model</A><BR>
6.9 <A HREF = "#6_9">SPC water model</A><BR>
6.10 <A HREF = "#6_10">Coupling LAMMPS to other codes</A><BR>
6.11 <A HREF = "#6_11">Visualizing LAMMPS snapshots</A><BR>
6.12 <A HREF = "#6_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
6.13 <A HREF = "#6_13">NEMD simulations</A><BR>
6.14 <A HREF = "#6_14">Extended spherical and aspherical particles</A><BR>
6.15 <A HREF = "#6_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
6.16 <A HREF = "#6_16">Thermostatting, barostatting and computing temperature</A><BR>
6.17 <A HREF = "#6_17">Walls</A><BR>
6.18 <A HREF = "#6_18">Elastic constants</A><BR>
6.19 <A HREF = "#6_19">Library interface to LAMMPS</A><BR>
6.20 <A HREF = "#6_20">Calculating thermal conductivity</A><BR>
6.21 <A HREF = "#6_21">Calculating viscosity</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -42,7 +42,7 @@ setup and run various kinds of simulations.
</P>
<HR>
<A NAME = "4_1"></A><H4>4.1 Restarting a simulation
<A NAME = "6_1"></A><H4>6.1 Restarting a simulation
</H4>
<P>There are 3 ways to continue a long LAMMPS simulation. Multiple
<A HREF = "run.html">run</A> commands can be used in the same input script. Each
@ -134,7 +134,7 @@ but not in data files.
</P>
<HR>
<A NAME = "4_2"></A><H4>4.2 2d simulations
<A NAME = "6_2"></A><H4>6.2 2d simulations
</H4>
<P>Use the <A HREF = "dimension.html">dimension</A> command to specify a 2d simulation.
</P>
@ -169,7 +169,7 @@ the same as in 3d.
</P>
<HR>
<A NAME = "4_3"></A><H4>4.3 CHARMM, AMBER, and DREIDING force fields
<A NAME = "6_3"></A><H4>6.3 CHARMM, AMBER, and DREIDING force fields
</H4>
<P>A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
@ -246,7 +246,7 @@ documentation for the formula it computes.
</UL>
<HR>
<A NAME = "4_4"></A><H4>4.4 Running multiple simulations from one input script
<A NAME = "6_4"></A><H4>6.4 Running multiple simulations from one input script
</H4>
<P>This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
@ -334,7 +334,7 @@ the 4th simulation, and so forth, until all 8 were completed.
</P>
<HR>
<A NAME = "4_5"></A><H4>4.5 Multi-replica simulations
<A NAME = "6_5"></A><H4>6.5 Multi-replica simulations
</H4>
<P>Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
@ -381,7 +381,7 @@ physical processors.
</P>
<HR>
<A NAME = "4_6"></A><H4>4.6 Granular models
<A NAME = "6_6"></A><H4>6.6 Granular models
</H4>
<P>Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
@ -398,7 +398,7 @@ the following commands:
</P>
<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</UL>
<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#4_15">output with
<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#6_15">output with
thermodynamic info</A>.
</P>
<P>Use one of these 3 pair potentials, which compute forces and torques
@ -426,7 +426,7 @@ computations between frozen atoms by using this command:
</UL>
<HR>
<A NAME = "4_7"></A><H4>4.7 TIP3P water model
<A NAME = "6_7"></A><H4>6.7 TIP3P water model
</H4>
<P>The TIP3P water model as implemented in CHARMM
<A HREF = "#MacKerell">(MacKerell)</A> specifies a 3-site rigid water molecule with
@ -486,7 +486,7 @@ models</A>.
</P>
<HR>
<A NAME = "4_8"></A><H4>4.8 TIP4P water model
<A NAME = "6_8"></A><H4>6.8 TIP4P water model
</H4>
<P>The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
@ -545,7 +545,7 @@ models</A>.
</P>
<HR>
<A NAME = "4_9"></A><H4>4.9 SPC water model
<A NAME = "6_9"></A><H4>6.9 SPC water model
</H4>
<P>The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
@ -590,7 +590,7 @@ models</A>.
</P>
<HR>
<A NAME = "4_10"></A><H4>4.10 Coupling LAMMPS to other codes
<A NAME = "6_10"></A><H4>6.10 Coupling LAMMPS to other codes
</H4>
<P>LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
@ -673,7 +673,7 @@ the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#4_19">this section</A> of the manual
to LAMMPS. See <A HREF = "Section_howto.html#6_19">this section</A> of the manual
for a description of the interface and how to extend it for your
needs.
</P>
@ -690,7 +690,7 @@ instances of LAMMPS to perform different calculations.
</P>
<HR>
<A NAME = "4_11"></A><H4>4.11 Visualizing LAMMPS snapshots
<A NAME = "6_11"></A><H4>6.11 Visualizing LAMMPS snapshots
</H4>
<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
@ -749,7 +749,7 @@ See the <A HREF = "dump.html">dump</A> command for more information on XTC files
<HR>
<A NAME = "4_12"></A><H4>4.12 Triclinic (non-orthogonal) simulation boxes
<A NAME = "6_12"></A><H4>6.12 Triclinic (non-orthogonal) simulation boxes
</H4>
<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
@ -882,7 +882,7 @@ on non-equilibrium MD (NEMD) simulations.
</P>
<HR>
<A NAME = "4_13"></A><H4>4.13 NEMD simulations
<A NAME = "6_13"></A><H4>6.13 NEMD simulations
</H4>
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
@ -920,7 +920,7 @@ profile consistent with the applied shear strain rate.
</P>
<HR>
<A NAME = "4_14"></A><H4>4.14 Extended spherical and aspherical particles
<A NAME = "6_14"></A><H4>6.14 Extended spherical and aspherical particles
</H4>
<P>Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size
@ -1100,7 +1100,7 @@ particles are point masses.
</P>
<HR>
<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
<A NAME = "6_15"></A><H4>6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
</H4>
<P>There are four basic kinds of LAMMPS output:
</P>
@ -1394,7 +1394,7 @@ vector input could be a column of an array.
<HR>
<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
<A NAME = "6_16"></A><H4>6.16 Thermostatting, barostatting, and computing temperature
</H4>
<P>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
@ -1455,7 +1455,7 @@ thermostatting can be invoked via the <I>dpd/tstat</I> pair style:
<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the <A HREF = "#4_13">NEMD
integrates the SLLOD equations of motion. See the <A HREF = "#6_13">NEMD
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
nvt/asphere</A> thermostat not only translation
@ -1545,7 +1545,7 @@ thermodynamic output.
</P>
<HR>
<A NAME = "4_17"></A><H4>4.17 Walls
<A NAME = "6_17"></A><H4>6.17 Walls
</H4>
<P>Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
@ -1619,7 +1619,7 @@ frictional walls, as well as triangulated surfaces.
</P>
<HR>
<A NAME = "4_18"></A><H4>4.18 Elastic constants
<A NAME = "6_18"></A><H4>6.18 Elastic constants
</H4>
<P>Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
@ -1655,11 +1655,11 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
</P>
<HR>
<A NAME = "4_19"></A><H4>4.19 Library interface to LAMMPS
<A NAME = "6_19"></A><H4>6.19 Library interface to LAMMPS
</H4>
<P>As described in <A HREF = "Section_start.html#2_4">this section</A>, LAMMPS can be
built as a library, so that it can be called by another code, used in
a <A HREF = "Section_howto.html#4_10">coupled manner</A> with other codes, or driven
a <A HREF = "Section_howto.html#6_10">coupled manner</A> with other codes, or driven
through a <A HREF = "Section_python.html">Python interface</A>.
</P>
<P>All of these methodologies use a C-style interface to LAMMPS that is
@ -1735,10 +1735,10 @@ grab data from LAMMPS, change it, and put it back into LAMMPS.
</P>
<HR>
<A NAME = "4_20"></A><H4>4.20 Calculating thermal conductivity
<A NAME = "6_20"></A><H4>6.20 Calculating thermal conductivity
</H4>
<P>The thermal conductivity kappa of a material can be measured in at
least 3 ways using various options in LAMMPS. (See <A HREF = "Section_howto.html#4_21">this
least 3 ways using various options in LAMMPS. (See <A HREF = "Section_howto.html#6_21">this
section</A> of the manual for an analogous
discussion for viscosity). The thermal conducitivity tensor kappa is
a measure of the propensity of a material to transmit heat energy in a
@ -1755,7 +1755,7 @@ scalar.
<P>The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a <A HREF = "Section_howto.html#4_13">thermostatting fix</A>, the energy added
with a <A HREF = "Section_howto.html#6_13">thermostatting fix</A>, the energy added
to the hot region should equal the energy subtracted from the cold
region and be proportional to the heat flux moving between the
regions. See the paper by <A HREF = "#Ikeshoji">Ikeshoji and Hafskjold</A> for
@ -1800,10 +1800,10 @@ formalism.
</P>
<HR>
<A NAME = "4_21"></A><H4>4.21 Calculating viscosity
<A NAME = "6_21"></A><H4>6.21 Calculating viscosity
</H4>
<P>The shear viscosity eta of a fluid can be measured in at least 3 ways
using various options in LAMMPS. (See <A HREF = "Section_howto.html#4_20">this
using various options in LAMMPS. (See <A HREF = "Section_howto.html#6_20">this
section</A> of the manual for an analogous
discussion for thermal conductivity). Eta is a measure of the
propensity of a fluid to transmit momentum in a direction
@ -1829,7 +1829,7 @@ y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. In this case, the Pxy off-diagonal component of the pressure
or stress tensor, as calculated by the <A HREF = "compute_pressure.html">compute
pressure</A> command, can also be monitored, which
is the J term in the equation above. See <A HREF = "Section_howto.html#4_13">this
is the J term in the equation above. See <A HREF = "Section_howto.html#6_13">this
section</A> of the manual for details on NEMD
simulations.
</P>

104
doc/Section_howto.txt
View File

@ -1,4 +1,4 @@
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c
"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -6,32 +6,32 @@
:line
4. How-to discussions :h3
6. How-to discussions :h3
The following sections describe how to use various options within
LAMMPS.
4.1 "Restarting a simulation"_#4_1
4.2 "2d simulations"_#4_2
4.3 "CHARMM, AMBER, and DREIDING force fields"_#4_3
4.4 "Running multiple simulations from one input script"_#4_4
4.5 "Multi-replica simulations"_#4_5
4.6 "Granular models"_#4_6
4.7 "TIP3P water model"_#4_7
4.8 "TIP4P water model"_#4_8
4.9 "SPC water model"_#4_9
4.10 "Coupling LAMMPS to other codes"_#4_10
4.11 "Visualizing LAMMPS snapshots"_#4_11
4.12 "Triclinic (non-orthogonal) simulation boxes"_#4_12
4.13 "NEMD simulations"_#4_13
4.14 "Extended spherical and aspherical particles"_#4_14
4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#4_15
4.16 "Thermostatting, barostatting and computing temperature"_#4_16
4.17 "Walls"_#4_17
4.18 "Elastic constants"_#4_18
4.19 "Library interface to LAMMPS"_#4_19
4.20 "Calculating thermal conductivity"_#4_20
4.21 "Calculating viscosity"_#4_21 :all(b)
6.1 "Restarting a simulation"_#6_1
6.2 "2d simulations"_#6_2
6.3 "CHARMM, AMBER, and DREIDING force fields"_#6_3
6.4 "Running multiple simulations from one input script"_#6_4
6.5 "Multi-replica simulations"_#6_5
6.6 "Granular models"_#6_6
6.7 "TIP3P water model"_#6_7
6.8 "TIP4P water model"_#6_8
6.9 "SPC water model"_#6_9
6.10 "Coupling LAMMPS to other codes"_#6_10
6.11 "Visualizing LAMMPS snapshots"_#6_11
6.12 "Triclinic (non-orthogonal) simulation boxes"_#6_12
6.13 "NEMD simulations"_#6_13
6.14 "Extended spherical and aspherical particles"_#6_14
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#6_15
6.16 "Thermostatting, barostatting and computing temperature"_#6_16
6.17 "Walls"_#6_17
6.18 "Elastic constants"_#6_18
6.19 "Library interface to LAMMPS"_#6_19
6.20 "Calculating thermal conductivity"_#6_20
6.21 "Calculating viscosity"_#6_21 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -39,7 +39,7 @@ setup and run various kinds of simulations.
:line
4.1 Restarting a simulation :link(4_1),h4
6.1 Restarting a simulation :link(6_1),h4
There are 3 ways to continue a long LAMMPS simulation. Multiple
"run"_run.html commands can be used in the same input script. Each
@ -131,7 +131,7 @@ but not in data files.
:line
4.2 2d simulations :link(4_2),h4
6.2 2d simulations :link(6_2),h4
Use the "dimension"_dimension.html command to specify a 2d simulation.
@ -166,7 +166,7 @@ the same as in 3d.
:line
4.3 CHARMM, AMBER, and DREIDING force fields :link(4_3),h4
6.3 CHARMM, AMBER, and DREIDING force fields :link(6_3),h4
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
@ -242,7 +242,7 @@ documentation for the formula it computes.
:line
4.4 Running multiple simulations from one input script :link(4_4),h4
6.4 Running multiple simulations from one input script :link(6_4),h4
This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
@ -330,7 +330,7 @@ the 4th simulation, and so forth, until all 8 were completed.
:line
4.5 Multi-replica simulations :link(4_5),h4
6.5 Multi-replica simulations :link(6_5),h4
Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
@ -377,7 +377,7 @@ physical processors.
:line
4.6 Granular models :link(4_6),h4
6.6 Granular models :link(6_6),h4
Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
@ -395,7 +395,7 @@ This compute
"compute erotate/sphere"_compute_erotate_sphere.html :ul
calculates rotational kinetic energy which can be "output with
thermodynamic info"_Section_howto.html#4_15.
thermodynamic info"_Section_howto.html#6_15.
Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
@ -422,7 +422,7 @@ computations between frozen atoms by using this command:
:line
4.7 TIP3P water model :link(4_7),h4
6.7 TIP3P water model :link(6_7),h4
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
@ -482,7 +482,7 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
4.8 TIP4P water model :link(4_8),h4
6.8 TIP4P water model :link(6_8),h4
The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
@ -541,7 +541,7 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
4.9 SPC water model :link(4_9),h4
6.9 SPC water model :link(6_9),h4
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
@ -586,7 +586,7 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
4.10 Coupling LAMMPS to other codes :link(4_10),h4
6.10 Coupling LAMMPS to other codes :link(6_10),h4
LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
@ -668,7 +668,7 @@ the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "this section"_Section_howto.html#4_19 of the manual
to LAMMPS. See "this section"_Section_howto.html#6_19 of the manual
for a description of the interface and how to extend it for your
needs.
@ -685,7 +685,7 @@ instances of LAMMPS to perform different calculations.
:line
4.11 Visualizing LAMMPS snapshots :link(4_11),h4
6.11 Visualizing LAMMPS snapshots :link(6_11),h4
LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
@ -741,7 +741,7 @@ See the "dump"_dump.html command for more information on XTC files.
:line
4.12 Triclinic (non-orthogonal) simulation boxes :link(4_12),h4
6.12 Triclinic (non-orthogonal) simulation boxes :link(6_12),h4
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
@ -874,7 +874,7 @@ on non-equilibrium MD (NEMD) simulations.
:line
4.13 NEMD simulations :link(4_13),h4
6.13 NEMD simulations :link(6_13),h4
Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
@ -912,7 +912,7 @@ An alternative method for calculating viscosities is provided via the
:line
4.14 Extended spherical and aspherical particles :link(4_14),h4
6.14 Extended spherical and aspherical particles :link(6_14),h4
Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size
@ -1092,7 +1092,7 @@ particles are point masses.
:line
4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(4_15),h4
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(6_15),h4
There are four basic kinds of LAMMPS output:
@ -1382,7 +1382,7 @@ Command: Input: Output:
:line
4.16 Thermostatting, barostatting, and computing temperature :link(4_16),h4
6.16 Thermostatting, barostatting, and computing temperature :link(6_16),h4
Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
@ -1444,7 +1444,7 @@ thermostatting can be invoked via the {dpd/tstat} pair style:
particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the "NEMD
simulations"_#4_13 section of this page for further details. "Fix
simulations"_#6_13 section of this page for further details. "Fix
nvt/sphere"_fix_nvt_sphere.html and "fix
nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
@ -1533,7 +1533,7 @@ thermodynamic output.
:line
4.17 Walls :link(4_17),h4
6.17 Walls :link(6_17),h4
Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
@ -1607,7 +1607,7 @@ frictional walls, as well as triangulated surfaces.
:line
4.18 Elastic constants :link(4_18),h4
6.18 Elastic constants :link(6_18),h4
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
@ -1643,11 +1643,11 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
:line
4.19 Library interface to LAMMPS :link(4_19),h4
6.19 Library interface to LAMMPS :link(6_19),h4
As described in "this section"_Section_start.html#2_4, LAMMPS can be
built as a library, so that it can be called by another code, used in
a "coupled manner"_Section_howto.html#4_10 with other codes, or driven
a "coupled manner"_Section_howto.html#6_10 with other codes, or driven
through a "Python interface"_Section_python.html.
All of these methodologies use a C-style interface to LAMMPS that is
@ -1723,11 +1723,11 @@ grab data from LAMMPS, change it, and put it back into LAMMPS.
:line
4.20 Calculating thermal conductivity :link(4_20),h4
6.20 Calculating thermal conductivity :link(6_20),h4
The thermal conductivity kappa of a material can be measured in at
least 3 ways using various options in LAMMPS. (See "this
section"_Section_howto.html#4_21 of the manual for an analogous
section"_Section_howto.html#6_21 of the manual for an analogous
discussion for viscosity). The thermal conducitivity tensor kappa is
a measure of the propensity of a material to transmit heat energy in a
diffusive manner as given by Fourier's law
@ -1743,7 +1743,7 @@ scalar.
The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a "thermostatting fix"_Section_howto.html#4_13, the energy added
with a "thermostatting fix"_Section_howto.html#6_13, the energy added
to the hot region should equal the energy subtracted from the cold
region and be proportional to the heat flux moving between the
regions. See the paper by "Ikeshoji and Hafskjold"_#Ikeshoji for
@ -1788,11 +1788,11 @@ formalism.
:line
4.21 Calculating viscosity :link(4_21),h4
6.21 Calculating viscosity :link(6_21),h4
The shear viscosity eta of a fluid can be measured in at least 3 ways
using various options in LAMMPS. (See "this
section"_Section_howto.html#4_20 of the manual for an analogous
section"_Section_howto.html#6_20 of the manual for an analogous
discussion for thermal conductivity). Eta is a measure of the
propensity of a fluid to transmit momentum in a direction
perpendicular to the direction of velocity or momentum flow.
@ -1818,7 +1818,7 @@ dVx/dy. In this case, the Pxy off-diagonal component of the pressure
or stress tensor, as calculated by the "compute
pressure"_compute_pressure.html command, can also be monitored, which
is the J term in the equation above. See "this
section"_Section_howto.html#4_13 of the manual for details on NEMD
section"_Section_howto.html#6_13 of the manual for details on NEMD
simulations.
The second method is to perform a reverse non-equilibrium MD

88
doc/Section_modify.html
View File

@ -11,7 +11,7 @@ Section</A>
<HR>
<H3>8. Modifying & extending LAMMPS
<H3>10. Modifying & extending LAMMPS
</H3>
<P>LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 75% of its source code
@ -75,28 +75,9 @@ the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
</P>
<P>Here is a list of the new features that can be added in this way,
along with information about how to submit your features for inclusion
in the LAMMPS distribution.
</P>
<UL><LI><A HREF = "#atom">Atom styles</A>
<LI><A HREF = "#bond">Bond, angle, dihedral, improper potentials</A>
<LI><A HREF = "#compute">Compute styles</A>
<LI><A HREF = "#dump">Dump styles</A>
<LI><A HREF = "#dump">Dump custom output options</A>
<LI><A HREF = "#fix">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
<LI><A HREF = "#command">Input script commands</A>
<LI><A HREF = "#kspace">Kspace computations</A>
<LI><A HREF = "#min">Minimization solvers</A>
<LI><A HREF = "#pair">Pairwise potentials</A>
<LI><A HREF = "#region">Region styles</A>
<LI><A HREF = "#thermo">Thermodynamic output options</A>
<LI><A HREF = "#variable">Variable options</A>
</UL>
<UL><LI><A HREF = "#package">Submitting new features to the developers to include in LAMMPS</A>
</UL>
<P>As illustrated by the pairwise example, these options are referred to
in the LAMMPS documentation as the "style" of a particular command.
<P>As illustrated by this pairwise example, many kinds of options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
</P>
<P>The instructions below give the header file for the base class that
these styles are derived from. Public variables in that file are ones
@ -108,13 +89,9 @@ LAMMPS expects. Virtual functions that are not set to 0 are functions
you can optionally define.
</P>
<P>Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained in
these sections:
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
below.
</P>
<UL><LI><A HREF = "#dump_custom">Dump custom output options</A>
<LI><A HREF = "#thermo">Thermodynamic output options</A>
<LI><A HREF = "#variable">Variable options</A>
</UL>
<HR>
<P>Here are additional guidelines for modifying LAMMPS and adding new
@ -136,13 +113,34 @@ command.
<LI>If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. We might be
interested in adding it to the LAMMPS distribution.
interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page.
</UL>
<HR>
<P>Here are the subsequent topics discussed below, most of which are new
features that can be added in the manner just described:
</P>
10.1 <A HREF = "#10_1">Atom styles</A><BR>
10.2 <A HREF = "#10_2">Bond, angle, dihedral, improper potentials</A><BR>
10.3 <A HREF = "#10_3">Compute styles</A><BR>
10.4 <A HREF = "#10_4">Dump styles</A><BR>
10.5 <A HREF = "#10_5">Dump custom output options</A><BR>
10.6 <A HREF = "#10_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
10.7 <A HREF = "10_7">Input script commands</A><BR>
10.8 <A HREF = "#10_8">Kspace computations</A><BR>
10.9 <A HREF = "#10_9">Minimization styles</A><BR>
10.10 <A HREF = "#10_10">Pairwise potentials</A><BR>
10.11 <A HREF = "#10_11">Region styles</A><BR>
10.12 <A HREF = "#10_12">Thermodynamic output options</A><BR>
10.13 <A HREF = "#10_13">Variable options</A><BR>
10.14 <A HREF = "#10_14">Submitting new features for inclusion in LAMMPS</A> <BR>
<HR>
<A NAME = "atom"></A><H4>Atom styles
<HR>
<A NAME = "10_1"></A><H4>10.1 Atom styles
</H4>
<P>Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
@ -192,7 +190,7 @@ modify.
</P>
<HR>
<A NAME = "bond"></A><H4>Bond, angle, dihedral, improper potentials
<A NAME = "10_2"></A><H4>10.2 Bond, angle, dihedral, improper potentials
</H4>
<P>Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
@ -216,7 +214,7 @@ details.
<HR>
<A NAME = "compute"></A><H4>Compute styles
<A NAME = "10_3"></A><H4>10.3 Compute styles
</H4>
<P>Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
@ -244,9 +242,9 @@ class. See compute.h for details.
<HR>
<A NAME = "dump"></A><H4>Dump styles
<A NAME = "10_4"></A><H4>10.4 Dump styles
</H4>
<A NAME = "dump_custom"></A><H4>Dump custom output options
<A NAME = "10_5"></A><H4>10.5 Dump custom output options
</H4>
<P>Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
@ -277,7 +275,7 @@ half-dozen or so locations where code will need to be added.
</P>
<HR>
<A NAME = "fix"></A><H4>Fix styles
<A NAME = "10_6"></A><H4>10.6 Fix styles
</H4>
<P>In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
@ -355,7 +353,7 @@ quantities and/or to be summed to the potential energy of the system.
</P>
<HR>
<A NAME = "command"></A><H4>Input script commands
<A NAME = "10_7"></A><H4>10.7 Input script commands
</H4>
<P>New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
@ -377,7 +375,7 @@ needed.
</P>
<HR>
<A NAME = "kspace"></A><H4>Kspace computations
<A NAME = "10_8"></A><H4>10.8 Kspace computations
</H4>
<P>Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
@ -397,7 +395,7 @@ class. See kspace.h for details.
<HR>
<A NAME = "min"></A><H4>Minimization solvers
<A NAME = "10_9"></A><H4>10.9 Minimization styles
</H4>
<P>Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
@ -416,7 +414,7 @@ class. See min.h for details.
<HR>
<A NAME = "pair"></A><H4>Pairwise potentials
<A NAME = "10_10"></A><H4>10.10 Pairwise potentials
</H4>
<P>Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
@ -445,7 +443,7 @@ includes some optional methods to enable its use with rRESPA.
</P>
<HR>
<A NAME = "region"></A><H4>Region styles
<A NAME = "10_11"></A><H4>10.11 Region styles
</H4>
<P>Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
@ -463,7 +461,7 @@ class. See region.h for details.
<HR>
<A NAME = "thermo"></A><H4>Thermodynamic output options
<A NAME = "10_12"></A><H4>10.12 Thermodynamic output options
</H4>
<P>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
@ -492,7 +490,7 @@ by adding a new keyword to the thermo command.
</P>
<HR>
<A NAME = "variable"></A><H4>Variable options
<A NAME = "10_13"></A><H4>10.13 Variable options
</H4>
<P>There is one class that computes and stores <A HREF = "variable.html">variable</A>
information in LAMMPS; see the file variable.cpp. The value
@ -532,7 +530,9 @@ then be accessed by variables) was discussed
</P>
<HR>
<A NAME = "package"></A><H4>Submitting new features to the developers to include in LAMMPS
<HR>
<A NAME = "10_14"></A><H4>10.14 Submitting new features for inclusion in LAMMPS
</H4>
<P>We encourage users to submit new features that they add to LAMMPS to
<A HREF = "http://lammps.sandia.gov/authors.html">the developers</A>, especially if

91
doc/Section_modify.txt
View File

@ -8,7 +8,7 @@ Section"_Section_python.html :c
:line
8. Modifying & extending LAMMPS :h3
10. Modifying & extending LAMMPS :h3
LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 75% of its source code
@ -72,30 +72,9 @@ the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
Here is a list of the new features that can be added in this way,
along with information about how to submit your features for inclusion
in the LAMMPS distribution.
"Atom styles"_#atom
"Bond, angle, dihedral, improper potentials"_#bond
"Compute styles"_#compute
"Dump styles"_#dump
"Dump custom output options"_#dump
"Fix styles"_#fix which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
"Input script commands"_#command
"Kspace computations"_#kspace
"Minimization solvers"_#min
"Pairwise potentials"_#pair
"Region styles"_#region
"Thermodynamic output options"_#thermo
"Variable options"_#variable :ul
"Submitting new features to the developers to include in LAMMPS"_#package :ul
As illustrated by the pairwise example, these options are referred to
in the LAMMPS documentation as the "style" of a particular command.
As illustrated by this pairwise example, many kinds of options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
The instructions below give the header file for the base class that
these styles are derived from. Public variables in that file are ones
@ -107,12 +86,8 @@ LAMMPS expects. Virtual functions that are not set to 0 are functions
you can optionally define.
Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained in
these sections:
"Dump custom output options"_#dump_custom
"Thermodynamic output options"_#thermo
"Variable options"_#variable :ul
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
below.
:line
@ -135,12 +110,35 @@ command. :l
If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
"developers"_http://lammps.sandia.gov/authors.html. We might be
interested in adding it to the LAMMPS distribution. :l,ule
interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page. :l,ule
:line
Here are the subsequent topics discussed below, most of which are new
features that can be added in the manner just described:
10.1 "Atom styles"_#10_1
10.2 "Bond, angle, dihedral, improper potentials"_#10_2
10.3 "Compute styles"_#10_3
10.4 "Dump styles"_#10_4
10.5 "Dump custom output options"_#10_5
10.6 "Fix styles"_#10_6 which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
10.7 "Input script commands"_10_7
10.8 "Kspace computations"_#10_8
10.9 "Minimization styles"_#10_9
10.10 "Pairwise potentials"_#10_10
10.11 "Region styles"_#10_11
10.12 "Thermodynamic output options"_#10_12
10.13 "Variable options"_#10_13
10.14 "Submitting new features for inclusion in LAMMPS"_#10_14 :all(b)
:line
:line
Atom styles :link(atom),h4
10.1 Atom styles :link(10_1),h4
Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
@ -188,7 +186,7 @@ modify.
:line
Bond, angle, dihedral, improper potentials :link(bond),h4
10.2 Bond, angle, dihedral, improper potentials :link(10_2),h4
Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
@ -210,7 +208,7 @@ single: force and energy of a single bond :tb(s=:)
:line
Compute styles :link(compute),h4
10.3 Compute styles :link(10_3),h4
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
@ -236,8 +234,8 @@ memory_usage: tally memory usage :tb(s=:)
:line
Dump styles :link(dump),h4
Dump custom output options :link(dump_custom),h4
10.4 Dump styles :link(10_4),h4
10.5 Dump custom output options :link(10_5),h4
Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
@ -266,7 +264,7 @@ half-dozen or so locations where code will need to be added.
:line
Fix styles :link(fix),h4
10.6 Fix styles :link(10_6),h4
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
@ -342,7 +340,7 @@ quantities and/or to be summed to the potential energy of the system.
:line
Input script commands :link(command),h4
10.7 Input script commands :link(10_7),h4
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
@ -362,7 +360,7 @@ needed.
:line
Kspace computations :link(kspace),h4
10.8 Kspace computations :link(10_8),h4
Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
@ -380,7 +378,7 @@ memory_usage: tally of memory usage :tb(s=:)
:line
Minimization solvers :link(min),h4
10.9 Minimization styles :link(10_9),h4
Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
@ -397,7 +395,7 @@ memory_usage: tally of memory usage :tb(s=:)
:line
Pairwise potentials :link(pair),h4
10.10 Pairwise potentials :link(10_10),h4
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
@ -424,7 +422,7 @@ The inner/middle/outer routines are optional.
:line
Region styles :link(region),h4
10.11 Region styles :link(10_11),h4
Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
@ -440,7 +438,7 @@ match: determine whether a point is in the region :tb(s=:)
:line
Thermodynamic output options :link(thermo),h4
10.12 Thermodynamic output options :link(10_12),h4
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
@ -469,7 +467,7 @@ by adding a new keyword to the thermo command.
:line
Variable options :link(variable),h4
10.13 Variable options :link(10_13),h4
There is one class that computes and stores "variable"_variable.html
information in LAMMPS; see the file variable.cpp. The value
@ -507,9 +505,10 @@ Adding new "compute styles"_compute.html (whose calculated values can
then be accessed by variables) was discussed
"here"_Section_modify.html#compute on this page.
:line
:line
Submitting new features to the developers to include in LAMMPS :link(package),h4
10.14 Submitting new features for inclusion in LAMMPS :link(10_14),h4
We encourage users to submit new features that they add to LAMMPS to
"the developers"_http://lammps.sandia.gov/authors.html, especially if

2
doc/Section_perf.html
View File

@ -9,7 +9,7 @@
<HR>
<H3>6. Performance & scalability
<H3>8. Performance & scalability
</H3>
<P>LAMMPS performance on several prototypical benchmarks and machines is
discussed on the Benchmarks page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> where

2
doc/Section_perf.txt
View File

@ -6,7 +6,7 @@
:line
6. Performance & scalability :h3
8. Performance & scalability :h3
LAMMPS performance on several prototypical benchmarks and machines is
discussed on the Benchmarks page of the "LAMMPS WWW Site"_lws where

32
doc/Section_python.html
View File

@ -1,5 +1,5 @@
<HTML>
<CENTER><A HREF = "Section_modify.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_accelerate.html">Next Section</A>
<CENTER><A HREF = "Section_modify.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 Section</A>
</CENTER>
@ -9,7 +9,7 @@
<HR>
<H3>9. Python interface to LAMMPS
<H3>11. Python interface to LAMMPS
</H3>
<P>The LAMMPS distribution includes some Python code in its python
directory which wraps the library interface to LAMMPS. This makes it
@ -88,13 +88,13 @@ setup discussion. The next to last sub-section describes the Python
syntax used to invoke LAMMPS. The last sub-section describes example
Python scripts included in the python directory.
</P>
<UL><LI><A HREF = "#9_1">Extending Python with a serial version of LAMMPS</A>
<LI><A HREF = "#9_2">Creating a shared MPI library</A>
<LI><A HREF = "#9_3">Extending Python with a parallel version of LAMMPS</A>
<LI><A HREF = "#9_4">Extending Python with MPI</A>
<LI><A HREF = "#9_5">Testing the Python-LAMMPS interface</A>
<LI><A HREF = "#9_6">Using LAMMPS from Python</A>
<LI><A HREF = "#9_7">Example Python scripts that use LAMMPS</A>
<UL><LI>11.1 <A HREF = "#11_1">Extending Python with a serial version of LAMMPS</A>
<LI>11.2 <A HREF = "#11_2">Creating a shared MPI library</A>
<LI>11.3 <A HREF = "#11_3">Extending Python with a parallel version of LAMMPS</A>
<LI>11.4 <A HREF = "#11_4">Extending Python with MPI</A>
<LI>11.5 <A HREF = "#11_5">Testing the Python-LAMMPS interface</A>
<LI>11.6 <A HREF = "#11_6">Using LAMMPS from Python</A>
<LI>11.7 <A HREF = "#11_7">Example Python scripts that use LAMMPS</A>
</UL>
<P>Before proceeding, there are 2 items to note.
</P>
@ -134,7 +134,7 @@ LAMMPS wrapper.
<HR>
<A NAME = "9_1"></A><H4>Extending Python with a serial version of LAMMPS
<A NAME = "11_1"></A><H4>11.1 Extending Python with a serial version of LAMMPS
</H4>
<P>From the python directory in the LAMMPS distribution, type
</P>
@ -164,7 +164,7 @@ this, where you should replace "foo" with your directory of choice.
</P>
<HR>
<A NAME = "9_2"></A><H4>Creating a shared MPI library
<A NAME = "11_2"></A><H4>11.2 Creating a shared MPI library
</H4>
<P>A shared library is one that is dynamically loadable, which is what
Python requires. On Linux this is a library file that ends in ".so",
@ -195,7 +195,7 @@ stand-alone code.
</P>
<HR>
<A NAME = "9_3"></A><H4>Extending Python with a parallel version of LAMMPS
<A NAME = "11_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
</H4>
<P>From the python directory, type
</P>
@ -233,7 +233,7 @@ will be put in the appropriate directory.
</P>
<HR>
<A NAME = "9_4"></A><H4>Extending Python with MPI
<A NAME = "11_4"></A><H4>11.4 Extending Python with MPI
</H4>
<P>There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
@ -308,7 +308,7 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size())
</P>
<HR>
<A NAME = "9_5"></A><H4>Testing the Python-LAMMPS interface
<A NAME = "11_5"></A><H4>11.5 Testing the Python-LAMMPS interface
</H4>
<P>Before using LAMMPS in a Python program, one more step is needed. The
interface to LAMMPS is via the Python ctypes package, which loads the
@ -402,7 +402,7 @@ Python on a single processor, not in parallel.
<HR>
<A NAME = "9_6"></A><H4>Using LAMMPS from Python
<A NAME = "11_6"></A><H4>11.6 Using LAMMPS from Python
</H4>
<P>The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a
@ -594,7 +594,7 @@ Python script. Isn't ctypes amazing?
<HR>
<A NAME = "9_7"></A><H4>Example Python scripts that use LAMMPS
<A NAME = "11_7"></A><H4>11.7 Example Python scripts that use LAMMPS
</H4>
<P>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of

32
doc/Section_python.txt
View File

@ -1,4 +1,4 @@
"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_accelerate.html :c
"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -6,7 +6,7 @@
:line
9. Python interface to LAMMPS :h3
11. Python interface to LAMMPS :h3
The LAMMPS distribution includes some Python code in its python
directory which wraps the library interface to LAMMPS. This makes it
@ -85,13 +85,13 @@ setup discussion. The next to last sub-section describes the Python
syntax used to invoke LAMMPS. The last sub-section describes example
Python scripts included in the python directory.
"Extending Python with a serial version of LAMMPS"_#9_1
"Creating a shared MPI library"_#9_2
"Extending Python with a parallel version of LAMMPS"_#9_3
"Extending Python with MPI"_#9_4
"Testing the Python-LAMMPS interface"_#9_5
"Using LAMMPS from Python"_#9_6
"Example Python scripts that use LAMMPS"_#9_7 :ul
11.1 "Extending Python with a serial version of LAMMPS"_#11_1
11.2 "Creating a shared MPI library"_#11_2
11.3 "Extending Python with a parallel version of LAMMPS"_#11_3
11.4 "Extending Python with MPI"_#11_4
11.5 "Testing the Python-LAMMPS interface"_#11_5
11.6 "Using LAMMPS from Python"_#11_6
11.7 "Example Python scripts that use LAMMPS"_#11_7 :ul
Before proceeding, there are 2 items to note.
@ -130,7 +130,7 @@ LAMMPS wrapper.
:line
:line
Extending Python with a serial version of LAMMPS :link(9_1),h4
11.1 Extending Python with a serial version of LAMMPS :link(11_1),h4
From the python directory in the LAMMPS distribution, type
@ -160,7 +160,7 @@ If these commands are successful, a {lammps.py} and
:line
Creating a shared MPI library :link(9_2),h4
11.2 Creating a shared MPI library :link(11_2),h4
A shared library is one that is dynamically loadable, which is what
Python requires. On Linux this is a library file that ends in ".so",
@ -191,7 +191,7 @@ stand-alone code.
:line
Extending Python with a parallel version of LAMMPS :link(9_3),h4
11.3 Extending Python with a parallel version of LAMMPS :link(11_3),h4
From the python directory, type
@ -229,7 +229,7 @@ will be put in the appropriate directory.
:line
Extending Python with MPI :link(9_4),h4
11.4 Extending Python with MPI :link(11_4),h4
There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
@ -304,7 +304,7 @@ and see one line of output for each processor you ran on.
:line
Testing the Python-LAMMPS interface :link(9_5),h4
11.5 Testing the Python-LAMMPS interface :link(11_5),h4
Before using LAMMPS in a Python program, one more step is needed. The
interface to LAMMPS is via the Python ctypes package, which loads the
@ -397,7 +397,7 @@ Python on a single processor, not in parallel.
:line
:line
Using LAMMPS from Python :link(9_6),h4
11.6 Using LAMMPS from Python :link(11_6),h4
The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a
@ -588,7 +588,7 @@ Python script. Isn't ctypes amazing? :l,ule
:line
:line
Example Python scripts that use LAMMPS :link(9_7),h4
11.7 Example Python scripts that use LAMMPS :link(11_7),h4
These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of

2
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View File

@ -11,7 +11,7 @@ Section</A>
<HR>
<H3>7. Additional tools
<H3>9. Additional tools
</H3>
<P>LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing

2
doc/Section_tools.txt
View File

@ -8,7 +8,7 @@ Section"_Section_modify.html :c
:line
7. Additional tools :h3
9. Additional tools :h3
LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing