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W. Michael Brown
2011-10-26 19:47:51 -04:00
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1
README
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@ -39,3 +39,4 @@ Point your browser at any of these files to get started:
doc/Manual.html the LAMMPS manual
doc/Section_intro.html hi-level introduction to LAMMPS
doc/Section_start.html how to build and use LAMMPS
doc/Developer.pdf LAMMPS developer guide

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\documentstyle[12pt]{article}
\begin{document}
$$
T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = Delta
$$
\end{document}

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\documentclass[12pt]{article}
\usepackage{amssymb,amsmath}
\begin{document}
\begin{eqnarray*}
E & = & \sum_{j \ne i} \phi_{2}(R_{ij}, Z_{i}) + \sum_{j \ne i} \sum_{k \ne i,k > j} \phi_{3}(R_{ij}, R_{ik}, Z_{i}) \\
\phi_{2}(r, Z) & = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\
\phi_{3}(R_{ij}, R_{ik}, Z_i) & = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\
Z_i & = & \sum_{m \ne i} f(R_{im}) \qquad
f(r) = \begin{cases}
1 & \quad r<c \\
\exp\left(\frac{\alpha}{1-x^{-3}}\right) & \quad c<r<a \\
0 & \quad r>a
\end{cases} \\
h(l,Z) & = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\
Q(Z) & = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z})
\end{eqnarray*}
\end{document}

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doc/Eqs/pair_gromacs.tex
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@ -7,8 +7,8 @@ E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + S_{LJ}(r)
\qquad r < r_c \\
E_C & = & \frac{C q_i q_j}{\epsilon r} + S_C(r) \qquad r < r_c \\
S(r) & = & 0 \qquad r < r_1 \\
S(r) & = & A (r - r_1)^2 + B (r - r_1)^3 \qquad r_1 < r < r_c
S(r) & = & C \qquad r < r_1 \\
S(r) & = & \frac{A}{3} (r - r_1)^3 + \frac{B}{4} (r - r_1)^4 + C \qquad r_1 < r < r_c
\end{eqnarray*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\begin{eqnarray*}
E &=& u_{LJ}(r) \qquad r \leq r_s \\
&=& u_{LJ}(r_s) + (r-r_s) u'_{LJ}(r_s) - \frac{1}{6} A_3 (r-r_s)^3 \qquad r_s < r \leq r_c \\
&=& 0 \qquad r > r_c
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
p = (\gamma - 1) \rho e
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
p = B [(\frac{\rho}{\rho_0})^{\gamma} - 1]
$$
\end{document}

196
doc/Manual.html
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@ -42,6 +42,10 @@ describe the version you have.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of very patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
@ -78,89 +82,107 @@ it gives quick access to documentation for all LAMMPS commands.
</P>
<OL><LI><A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#1_1">What is LAMMPS</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#1_2">LAMMPS features</A>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#1_3">LAMMPS non-features</A>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#1_4">Open source distribution</A>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#1_5">Acknowledgments and citations</A>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#2_1">What's in the LAMMPS distribution</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#2_3">Making LAMMPS with optional packages</A>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#2_4">Building LAMMPS as a library</A>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS as a library</A>
<BR>
2.5 <A HREF = "Section_start.html#2_5">Running LAMMPS</A>
2.5 <A HREF = "Section_start.html#start_5">Running LAMMPS</A>
<BR>
2.6 <A HREF = "Section_start.html#2_6">Command-line options</A>
2.6 <A HREF = "Section_start.html#start_6">Command-line options</A>
<BR>
2.7 <A HREF = "Section_start.html#2_7">Screen output</A>
2.7 <A HREF = "Section_start.html#start_7">Screen output</A>
<BR>
2.8 <A HREF = "Section_start.html#2_8">Tips for users of previous versions</A>
2.8 <A HREF = "2_8">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#3_1">LAMMPS input script</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#3_2">Parsing rules</A>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#3_3">Input script structure</A>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#3_4">Commands listed by category</A>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#3_5">Commands listed alphabetically</A>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_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_accelerate.html#acc_1">OPT package</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">USER-OMP package</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">GPU package</A>
<BR>
5.4 <A HREF = "Section_accelerate.html#acc_4">USER-CUDA package</A>
<BR>
5.5 <A HREF = "Section_accelerate.html#acc_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_howto.html#howto_1">Restarting a simulation</A>
<BR>
4.2 <A HREF = "Section_howto.html#4_2">2d simulations</A>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
4.3 <A HREF = "Section_howto.html#4_3">CHARMM and AMBER force fields</A>
6.3 <A HREF = "Section_howto.html#howto_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 = "Section_howto.html#howto_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 = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
4.6 <A HREF = "Section_howto.html#4_6">Granular models</A>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
4.7 <A HREF = "Section_howto.html#4_7">TIP3P water model</A>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
4.8 <A HREF = "Section_howto.html#4_8">TIP4P water model</A>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
4.9 <A HREF = "Section_howto.html#4_9">SPC water model</A>
6.9 <A HREF = "Section_howto.html#howto_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 = "Section_howto.html#howto_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 = "Section_howto.html#howto_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 = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
4.13 <A HREF = "Section_howto.html#4_13">NEMD simulations</A>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
4.14 <A HREF = "Section_howto.html#4_14">Extended spherical and aspherical particles</A>
6.14 <A HREF = "Section_howto.html#howto_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 = "Section_howto.html#howto_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 = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
4.17 <A HREF = "Section_howto.html#4_17">Walls</A>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
4.18 <A HREF = "Section_howto.html#4_18">Elastic constants</A>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
4.19 <A HREF = "Section_howto.html#4_19">Library interface to LAMMPS</A>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
4.20 <A HREF = "Section_howto.html#4_20">Calculating thermal conductivity</A>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
4.21 <A HREF = "Section_howto.html#4_21">Calculating viscosity</A>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
@ -170,45 +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_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Thermodynamic output options</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Variable options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_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 = "Section_python.html#py_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 = "Section_python.html#py_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 = "Section_python.html#py_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 = "Section_python.html#py_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 = "Section_python.html#py_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 = "Section_python.html#py_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 = "Section_python.html#py_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_errors.html#err_1">Common problems</A>
<BR>
11.2 <A HREF = "Section_errors.html#11_2">Reporting bugs</A>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
11.3 <A HREF = "Section_errors.html#11_3">Error & warning messages</A>
12.3 <A HREF = "Section_errors.html#err_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_history.html#hist_1">Coming attractions</A>
<BR>
12.2 <A HREF = "Section_history.html#12_2">Past versions</A>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
@ -301,6 +341,40 @@ it gives quick access to documentation for all LAMMPS commands.

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@ -38,7 +38,11 @@ describe the version you have. :l
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of very patch. :ule,l
it to be part of very patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :ule,l
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
@ -73,135 +77,172 @@ it gives quick access to documentation for all LAMMPS commands.
"htmldoc"_http://www.easysw.com/htmldoc
"Introduction"_Section_intro.html :olb,l
1.1 "What is LAMMPS"_1_1 :ulb,b
1.2 "LAMMPS features"_1_2 :b
1.3 "LAMMPS non-features"_1_3 :b
1.4 "Open source distribution"_1_4 :b
1.5 "Acknowledgments and citations"_1_5 :ule,b
1.1 "What is LAMMPS"_intro_1 :ulb,b
1.2 "LAMMPS features"_intro_2 :b
1.3 "LAMMPS non-features"_intro_3 :b
1.4 "Open source distribution"_intro_4 :b
1.5 "Acknowledgments and citations"_intro_5 :ule,b
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_2_1 :ulb,b
2.2 "Making LAMMPS"_2_2 :b
2.3 "Making LAMMPS with optional packages"_2_3 :b
2.4 "Building LAMMPS as a library"_2_4 :b
2.5 "Running LAMMPS"_2_5 :b
2.6 "Command-line options"_2_6 :b
2.7 "Screen output"_2_7 :b
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
2.3 "Making LAMMPS with optional packages"_start_3 :b
2.4 "Building LAMMPS as a library"_start_4 :b
2.5 "Running LAMMPS"_start_5 :b
2.6 "Command-line options"_start_6 :b
2.7 "Screen output"_start_7 :b
2.8 "Tips for users of previous versions"_2_8 :ule,b
"Commands"_Section_commands.html :l
3.1 "LAMMPS input script"_3_1 :ulb,b
3.2 "Parsing rules"_3_2 :b
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
3.1 "LAMMPS input script"_cmd_1 :ulb,b
3.2 "Parsing rules"_cmd_2 :b
3.3 "Input script structure"_cmd_3 :b
3.4 "Commands listed by category"_cmd_4 :b
3.5 "Commands listed alphabetically"_cmd_5 :ule,b
"Packages"_Section_packages.html :l
4.1 "Standard packages"_pkg_1 :ulb,b
4.2 "User packages"_pkg_2 :ule,b
"Using accelerated CPU and GPU styles"_Section_accelerate.html :l
5.1 "OPT package"_acc_1 :ulb,b
5.2 "USER-OMP package"_acc_2 :b
5.3 "GPU package"_acc_3 :b
5.4 "USER-CUDA package"_acc_4 :b
5.5 "Comparison of GPU and USER-CUDA packages"_acc_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"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
6.3 "CHARMM and AMBER force fields"_howto_3 :b
6.4 "Running multiple simulations from one input script"_howto_4 :b
6.5 "Multi-replica simulations"_howto_5 :b
6.6 "Granular models"_howto_6 :b
6.7 "TIP3P water model"_howto_7 :b
6.8 "TIP4P water model"_howto_8 :b
6.9 "SPC water model"_howto_9 :b
6.10 "Coupling LAMMPS to other codes"_howto_10 :b
6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
6.13 "NEMD simulations"_howto_13 :b
6.14 "Extended spherical and aspherical particles"_howto_14 :b
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
6.17 "Walls"_howto_17 :b
6.18 "Elastic constants"_howto_18 :b
6.19 "Library interface to LAMMPS"_howto_19 :b
6.20 "Calculating thermal conductivity"_howto_20 :b
6.21 "Calculating viscosity"_howto_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"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
10.3 "Compute styles"_mod_3 :b
10.4 "Dump styles"_mod_4 :b
10.5 "Dump custom output options"_mod_5 :b
10.6 "Fix styles"_mod_6 :b
10.7 "Input script commands"_mod_7 :b
10.8 "Kspace computations"_mod_8 :b
10.9 "Minimization styles"_mod_9 :b
10.10 "Pairwise potentials"_mod_10 :b
10.11 "Region styles"_mod_11 :b
10.12 "Thermodynamic output options"_mod_12 :b
10.13 "Variable options"_mod_13 :b
10.14 "Submitting new features for inclusion in LAMMPS"_mod_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"_py_1 :ulb,b
11.2 "Creating a shared MPI library"_py_2 :b
11.3 "Extending Python with a parallel version of LAMMPS"_py_3 :b
11.4 "Extending Python with MPI"_py_4 :b
11.5 "Testing the Python-LAMMPS interface"_py_5 :b
11.6 "Using LAMMPS from Python"_py_6 :b
11.7 "Example Python scripts that use LAMMPS"_py_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"_err_1 :ulb,b
12.2 "Reporting bugs"_err_2 :b
12.3 "Error & warning messages"_err_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"_hist_1 :ulb,b
13.2 "Past versions"_hist_2 :ule,b
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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
@ -36,7 +36,7 @@ style exist in LAMMPS:
</UL>
<P>Assuming you have built LAMMPS with the appropriate package, these
styles can be invoked by specifying them explicitly in your input
script. Or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
script. Or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> to invoke the accelerated versions
automatically, without changing your input script. The
<A HREF = "suffix.html">suffix</A> command allows you to set a suffix explicitly and
@ -47,10 +47,11 @@ input script.
speed-up the pairwise calculations of your simulation by 5-25%.
</P>
<P>Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in threaded mode using OpenMP. This can be
useful on nodes with high-core counts when using less MPI processes
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors.
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication.
</P>
<P>Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
@ -58,9 +59,9 @@ The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
</P>
<P>To see what styles are currently available in each of the accelerated
packages, see <A HREF = "Section_commands.html#3_5">this section</A> of the manual.
A list of accelerated styles is included in the pair, fix, compute,
and kspace sections.
packages, see <A HREF = "Section_commands.html#cmd_5">this section</A> of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
</P>
<P>The following sections explain:
</P>
@ -73,17 +74,17 @@ 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>
10.5 <A HREF = "#10_2">USER-OMP package</A><BR>
10.2 <A HREF = "#10_3">GPU package</A><BR>
10.3 <A HREF = "#10_4">USER-CUDA package</A><BR>
10.4 <A HREF = "#10_4">Comparison of GPU and USER-CUDA packages</A> <BR>
5.1 <A HREF = "#acc_1">OPT package</A><BR>
5.2 <A HREF = "#acc_2">USER-OMP package</A><BR>
5.3 <A HREF = "#acc_3">GPU package</A><BR>
5.4 <A HREF = "#acc_4">USER-CUDA package</A><BR>
5.5 <A HREF = "#acc_5">Comparison of GPU and USER-CUDA packages</A> <BR>
<HR>
<HR>
<H4><A NAME = "10_1"></A>10.1 OPT package
<H4><A NAME = "acc_1"></A>5.1 OPT package
</H4>
<P>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@ -112,16 +113,128 @@ to 20% savings.
<HR>
<H4><A NAME = "10_2"></A>10.2 USER-OMP package
<H4><A NAME = "acc_2"></A>5.2 USER-OMP package
</H4>
<P>This section will be written when the USER-OMP package is released
in main LAMMPS.
<P>The USER-OMP package was developed by Axel Kohlmeyer at Temple University.
It provides multi-threaded versions of most pair styles, all dihedral
styles and a few fixes in LAMMPS. The package currently uses the OpenMP
interface which requires using a specific compiler flag in the makefile
to enable multiple threads; without this flag the corresponding pair
styles will still be compiled and work, but do not support multi-threading.
</P>
<P><B>Building LAMMPS with the USER-OMP package:</B>
</P>
<P>The procedure for building LAMMPS with the USER-OMP package is simple.
You have to edit your machine specific makefile to add the flag to
enable OpenMP support to the CCFLAGS and LINKFLAGS variables. For the
GNU compilers for example this flag is called <I>-fopenmp</I>. Check your
compiler documentation to find out which flag you need to add.
The rest of the compilation is the same as for any other package which
has no additional library dependencies:
</P>
<PRE>make yes-user-omp
make machine
</PRE>
<P>Please note that this will only install accelerated versions
of styles that are already installed, so you want to install
this package as the last package, or else you may be missing
some accelerated styles. If you plan to uninstall some package,
you should first uninstall the USER-OMP package then the other
package and then re-install USER-OMP, to make sure that there
are no orphaned <I>omp</I> style files present, which would lead to
compilation errors.
</P>
<P>If your input script uses one of regular styles that are also
exist as an OpenMP version in the USER-OMP package you can run
it as follows:
</P>
<PRE>env OMP_NUM_THREADS=4 lmp_serial -sf omp -in in.script
env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
</PRE>
<P>The value of the environment variable OMP_NUM_THREADS determines how
many threads per MPI task are launched. All three examples above use
a total of 4 CPU cores. For different MPI implementations the method
to pass the OMP_NUM_THREADS environment variable to all processes is
different. Two different variants, one for MPICH and OpenMPI, respectively
are shown above. Please check the documentation of your MPI installation
for additional details. Alternatively, the value provided by OMP_NUM_THREADS
can be overridded with the <A HREF = "package.html">package omp</A> command.
Depending on which styles are accelerated in your input, you should
see a reduction in the "Pair time" and/or "Bond time" and "Loop time"
printed out at the end of the run. The optimal ratio of MPI to OpenMP
can vary a lot and should always be confirmed through some benchmark
runs for the current system and on the current machine.
</P>
<P><B>Restrictions:</B>
</P>
<P>None of the pair styles in the USER-OMP package support the "inner",
"middle", "outer" options for r-RESPA integration, only the "pair"
option is supported.
</P>
<P><B>Parallel efficiency and performance tips:</B>
</P>
<P>In most simple cases the MPI parallelization in LAMMPS is more
efficient than multi-threading implemented in the USER-OMP package.
Also the parallel efficiency varies between individual styles.
On the other hand, in many cases you still want to use the <I>omp</I> version
- even when compiling or running without OpenMP support - since they
all contain optimizations similar to those in the OPT package, which
can result in serial speedup.
</P>
<P>Using multi-threading is most effective under the following circumstances:
</P>
<UL><LI>Individual compute nodes have a significant number of CPU cores
but the CPU itself has limited memory bandwidth, e.g. Intel Xeon 53xx
(Clovertown) and 54xx (Harpertown) quad core processors. Running
one MPI task per CPU core will result in significant performance
degradation, so that running with 4 or even only 2 MPI tasks per
nodes is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way,
but offers and additional speedup from utilizing the otherwise
idle CPU cores.
<LI>The interconnect used for MPI communication is not able to provide
sufficient bandwidth for a large number of MPI tasks per node.
This applies for example to running over gigabit ethernet or
on Cray XT4 or XT5 series supercomputers. Same as in the aforementioned
case this effect worsens with using an increasing number of nodes.
<LI>The input is a system that has an inhomogeneous particle density
which cannot be mapped well to the domain decomposition scheme
that LAMMPS employs. While this can be to some degree alleviated
through using the <A HREF = "processors.html">processors</A> keyword, multi-threading
provides a parallelism that parallelizes over the number of particles
not their distribution in space.
<LI>Finally, multi-threaded styles can improve performance when running
LAMMPS in "capability mode", i.e. near the point where the MPI
parallelism scales out. This can happen in particular when using
as kspace style for long-range electrostatics. Here the scaling
of the kspace style is the performance limiting factor and using
multi-threaded styles allows to operate the kspace style at the
limit of scaling and then increase performance parallelizing
the real space calculations with hybrid MPI+OpenMP. Sometimes
additional speedup can be achived by increasing the real-space
coulomb cutoff and thus reducing the work in the kspace part.
</UL>
<P>The best parallel efficiency from <I>omp</I> styles is typically
achieved when there is at least one MPI task per physical
processor, i.e. socket or die.
</P>
<P>Using threads on hyper-threading enabled cores is usually
counterproductive, as the cost in additional memory bandwidth
requirements is not offset by the gain in CPU utilization
through hyper-threading.
</P>
<P>A description of the multi-threading strategy and some performance
examples are <A HREF = "http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented here</A>
</P>
<HR>
<HR>
<H4><A NAME = "10_3"></A>10.3 GPU package
<H4><A NAME = "acc_3"></A>5.3 GPU package
</H4>
<P>The GPU package was developed by Mike Brown at ORNL. It provides GPU
versions of several pair styles and for long-range Coulombics via the
@ -164,10 +277,10 @@ hardware and install specific NVIDIA CUDA software on your system:
</P>
<P>As with other packages that include a separately compiled library, you
need to first build the GPU library, before building LAMMPS itself.
General instructions for doing this are in <A HREF = "doc/Section_start.html#2_3">this
section</A> of the manual. For this package,
do the following, using a Makefile in lib/gpu appropriate for your
system:
General instructions for doing this are in <A HREF = "doc/Section_start.html#start_3">this
section</A> of the manual. For this
package, do the following, using a Makefile in lib/gpu appropriate for
your system:
</P>
<PRE>cd lammps/lib/gpu
make -f Makefile.linux
@ -201,7 +314,7 @@ and in many cases it will be more efficient to run this way.
</P>
<UL><LI>To invoke specific styles from the GPU package, you can either append
"gpu" to the style name (e.g. pair_style lj/cut/gpu), or use the
<A HREF = "Section_start.html#2_6">-suffix command-line switch</A>, or use the
<A HREF = "Section_start.html#start_6">-suffix command-line switch</A>, or use the
<A HREF = "suffix.html">suffix</A> command.
<LI>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I>.
@ -263,7 +376,7 @@ requires that your GPU card support double precision.
<HR>
<H4><A NAME = "10_4"></A>10.4 USER-CUDA package
<H4><A NAME = "acc_4"></A>5.4 USER-CUDA package
</H4>
<P>The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
@ -275,6 +388,9 @@ many timesteps, to run entirely on the GPU (except for inter-processor
MPI communication), so that atom-based data (e.g. coordinates, forces)
do not have to move back-and-forth between the CPU and GPU.
<LI>The speed-up advantage of this approach is typically better when the
number of atoms per GPU is large
<LI>Data will stay on the GPU until a timestep where a non-GPU-ized fix or
compute is invoked. Whenever a non-GPU operation occurs (fix,
compute, output), data automatically moves back to the CPU as needed.
@ -306,10 +422,10 @@ that its sample projects can be compiled without problems.
</P>
<P>As with other packages that include a separately compiled library, you
need to first build the USER-CUDA library, before building LAMMPS
itself. General instructions for doing this are in <A HREF = "doc/Section_start.html#2_3">this
section</A> of the manual. For this package,
do the following, using settings in the lib/cuda Makefiles appropriate
for your system:
itself. General instructions for doing this are in <A HREF = "doc/Section_start.html#start_3">this
section</A> of the manual. For this
package, do the following, using settings in the lib/cuda Makefiles
appropriate for your system:
</P>
<UL><LI>Go to the lammps/lib/cuda directory
@ -363,16 +479,16 @@ suffix are as follows:
</P>
<UL><LI>To invoke specific styles from the USER-CUDA package, you can either
append "cuda" to the style name (e.g. pair_style lj/cut/cuda), or use
the <A HREF = "Section_start.html#2_6">-suffix command-line switch</A>, or use the
<A HREF = "suffix.html">suffix</A> command. One exception is that the <A HREF = "kspace_style.html">kspace_style
pppm/cuda</A> command has to be requested
the <A HREF = "Section_start.html#start_6">-suffix command-line switch</A>, or use
the <A HREF = "suffix.html">suffix</A> command. One exception is that the
<A HREF = "kspace_style.html">kspace_style pppm/cuda</A> command has to be requested
explicitly.
<LI>To use the USER-CUDA package with its default settings, no additional
command is needed in your input script. This is because when LAMMPS
starts up, it detects if it has been built with the USER-CUDA package.
See the <A HREF = "Section_start.html#2_6">-cuda command-line switch</A> for more
details.
See the <A HREF = "Section_start.html#start_6">-cuda command-line switch</A> for
more details.
<LI>To change settings for the USER-CUDA package at run-time, the <A HREF = "package.html">package
cuda</A> command can be used near the beginning of your
@ -396,7 +512,7 @@ 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 = "acc_5"></A>5.5 Comparison of GPU and USER-CUDA packages
</H4>
<P>Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.

184
doc/Section_accelerate.txt
View File

@ -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
@ -34,7 +34,7 @@ style exist in LAMMPS:
Assuming you have built LAMMPS with the appropriate package, these
styles can be invoked by specifying them explicitly in your input
script. Or you can use the "-suffix command-line
switch"_Section_start.html#2_6 to invoke the accelerated versions
switch"_Section_start.html#start_6 to invoke the accelerated versions
automatically, without changing your input script. The
"suffix"_suffix.html command allows you to set a suffix explicitly and
to turn off/on the comand-line switch setting, both from within your
@ -44,10 +44,11 @@ Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25%.
Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in threaded mode using OpenMP. This can be
useful on nodes with high-core counts when using less MPI processes
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors.
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication.
Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
@ -55,9 +56,9 @@ The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
To see what styles are currently available in each of the accelerated
packages, see "this section"_Section_commands.html#3_5 of the manual.
A list of accelerated styles is included in the pair, fix, compute,
and kspace sections.
packages, see "this section"_Section_commands.html#cmd_5 of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
The following sections explain:
@ -70,16 +71,16 @@ 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
10.5 "USER-OMP package"_#10_2
10.2 "GPU package"_#10_3
10.3 "USER-CUDA package"_#10_4
10.4 "Comparison of GPU and USER-CUDA packages"_#10_4 :all(b)
5.1 "OPT package"_#acc_1
5.2 "USER-OMP package"_#acc_2
5.3 "GPU package"_#acc_3
5.4 "USER-CUDA package"_#acc_4
5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b)
:line
:line
10.1 OPT package :h4,link(10_1)
5.1 OPT package :h4,link(acc_1)
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@ -107,15 +108,127 @@ to 20% savings.
:line
:line
10.2 USER-OMP package :h4,link(10_2)
5.2 USER-OMP package :h4,link(acc_2)
This section will be written when the USER-OMP package is released
in main LAMMPS.
The USER-OMP package was developed by Axel Kohlmeyer at Temple University.
It provides multi-threaded versions of most pair styles, all dihedral
styles and a few fixes in LAMMPS. The package currently uses the OpenMP
interface which requires using a specific compiler flag in the makefile
to enable multiple threads; without this flag the corresponding pair
styles will still be compiled and work, but do not support multi-threading.
[Building LAMMPS with the USER-OMP package:]
The procedure for building LAMMPS with the USER-OMP package is simple.
You have to edit your machine specific makefile to add the flag to
enable OpenMP support to the CCFLAGS and LINKFLAGS variables. For the
GNU compilers for example this flag is called {-fopenmp}. Check your
compiler documentation to find out which flag you need to add.
The rest of the compilation is the same as for any other package which
has no additional library dependencies:
make yes-user-omp
make machine :pre
Please note that this will only install accelerated versions
of styles that are already installed, so you want to install
this package as the last package, or else you may be missing
some accelerated styles. If you plan to uninstall some package,
you should first uninstall the USER-OMP package then the other
package and then re-install USER-OMP, to make sure that there
are no orphaned {omp} style files present, which would lead to
compilation errors.
If your input script uses one of regular styles that are also
exist as an OpenMP version in the USER-OMP package you can run
it as follows:
env OMP_NUM_THREADS=4 lmp_serial -sf omp -in in.script
env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script :pre
The value of the environment variable OMP_NUM_THREADS determines how
many threads per MPI task are launched. All three examples above use
a total of 4 CPU cores. For different MPI implementations the method
to pass the OMP_NUM_THREADS environment variable to all processes is
different. Two different variants, one for MPICH and OpenMPI, respectively
are shown above. Please check the documentation of your MPI installation
for additional details. Alternatively, the value provided by OMP_NUM_THREADS
can be overridded with the "package omp"_package.html command.
Depending on which styles are accelerated in your input, you should
see a reduction in the "Pair time" and/or "Bond time" and "Loop time"
printed out at the end of the run. The optimal ratio of MPI to OpenMP
can vary a lot and should always be confirmed through some benchmark
runs for the current system and on the current machine.
[Restrictions:]
None of the pair styles in the USER-OMP package support the "inner",
"middle", "outer" options for r-RESPA integration, only the "pair"
option is supported.
[Parallel efficiency and performance tips:]
In most simple cases the MPI parallelization in LAMMPS is more
efficient than multi-threading implemented in the USER-OMP package.
Also the parallel efficiency varies between individual styles.
On the other hand, in many cases you still want to use the {omp} version
- even when compiling or running without OpenMP support - since they
all contain optimizations similar to those in the OPT package, which
can result in serial speedup.
Using multi-threading is most effective under the following circumstances:
Individual compute nodes have a significant number of CPU cores
but the CPU itself has limited memory bandwidth, e.g. Intel Xeon 53xx
(Clovertown) and 54xx (Harpertown) quad core processors. Running
one MPI task per CPU core will result in significant performance
degradation, so that running with 4 or even only 2 MPI tasks per
nodes is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way,
but offers and additional speedup from utilizing the otherwise
idle CPU cores. :ulb,l
The interconnect used for MPI communication is not able to provide
sufficient bandwidth for a large number of MPI tasks per node.
This applies for example to running over gigabit ethernet or
on Cray XT4 or XT5 series supercomputers. Same as in the aforementioned
case this effect worsens with using an increasing number of nodes. :l
The input is a system that has an inhomogeneous particle density
which cannot be mapped well to the domain decomposition scheme
that LAMMPS employs. While this can be to some degree alleviated
through using the "processors"_processors.html keyword, multi-threading
provides a parallelism that parallelizes over the number of particles
not their distribution in space. :l
Finally, multi-threaded styles can improve performance when running
LAMMPS in "capability mode", i.e. near the point where the MPI
parallelism scales out. This can happen in particular when using
as kspace style for long-range electrostatics. Here the scaling
of the kspace style is the performance limiting factor and using
multi-threaded styles allows to operate the kspace style at the
limit of scaling and then increase performance parallelizing
the real space calculations with hybrid MPI+OpenMP. Sometimes
additional speedup can be achived by increasing the real-space
coulomb cutoff and thus reducing the work in the kspace part. :l,ule
The best parallel efficiency from {omp} styles is typically
achieved when there is at least one MPI task per physical
processor, i.e. socket or die.
Using threads on hyper-threading enabled cores is usually
counterproductive, as the cost in additional memory bandwidth
requirements is not offset by the gain in CPU utilization
through hyper-threading.
A description of the multi-threading strategy and some performance
examples are "presented here"_http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1
:line
:line
10.3 GPU package :h4,link(10_3)
5.3 GPU package :h4,link(acc_3)
The GPU package was developed by Mike Brown at ORNL. It provides GPU
versions of several pair styles and for long-range Coulombics via the
@ -159,9 +272,9 @@ Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties :ul
As with other packages that include a separately compiled library, you
need to first build the GPU library, before building LAMMPS itself.
General instructions for doing this are in "this
section"_doc/Section_start.html#2_3 of the manual. For this package,
do the following, using a Makefile in lib/gpu appropriate for your
system:
section"_doc/Section_start.html#start_3 of the manual. For this
package, do the following, using a Makefile in lib/gpu appropriate for
your system:
cd lammps/lib/gpu
make -f Makefile.linux
@ -195,7 +308,7 @@ Additional input script requirements to run pair or PPPM styles with a
To invoke specific styles from the GPU package, you can either append
"gpu" to the style name (e.g. pair_style lj/cut/gpu), or use the
"-suffix command-line switch"_Section_start.html#2_6, or use the
"-suffix command-line switch"_Section_start.html#start_6, or use the
"suffix"_suffix.html command. :ulb,l
The "newton pair"_newton.html setting must be {off}. :l
@ -256,7 +369,7 @@ 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(acc_4)
The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
@ -268,6 +381,9 @@ many timesteps, to run entirely on the GPU (except for inter-processor
MPI communication), so that atom-based data (e.g. coordinates, forces)
do not have to move back-and-forth between the CPU and GPU. :ulb,l
The speed-up advantage of this approach is typically better when the
number of atoms per GPU is large :l
Data will stay on the GPU until a timestep where a non-GPU-ized fix or
compute is invoked. Whenever a non-GPU operation occurs (fix,
compute, output), data automatically moves back to the CPU as needed.
@ -300,9 +416,9 @@ that its sample projects can be compiled without problems.
As with other packages that include a separately compiled library, you
need to first build the USER-CUDA library, before building LAMMPS
itself. General instructions for doing this are in "this
section"_doc/Section_start.html#2_3 of the manual. For this package,
do the following, using settings in the lib/cuda Makefiles appropriate
for your system:
section"_doc/Section_start.html#start_3 of the manual. For this
package, do the following, using settings in the lib/cuda Makefiles
appropriate for your system:
Go to the lammps/lib/cuda directory :ulb,l
@ -356,16 +472,16 @@ suffix are as follows:
To invoke specific styles from the USER-CUDA package, you can either
append "cuda" to the style name (e.g. pair_style lj/cut/cuda), or use
the "-suffix command-line switch"_Section_start.html#2_6, or use the
"suffix"_suffix.html command. One exception is that the "kspace_style
pppm/cuda"_kspace_style.html command has to be requested
the "-suffix command-line switch"_Section_start.html#start_6, or use
the "suffix"_suffix.html command. One exception is that the
"kspace_style pppm/cuda"_kspace_style.html command has to be requested
explicitly. :ulb,l
To use the USER-CUDA package with its default settings, no additional
command is needed in your input script. This is because when LAMMPS
starts up, it detects if it has been built with the USER-CUDA package.
See the "-cuda command-line switch"_Section_start.html#2_6 for more
details. :l
See the "-cuda command-line switch"_Section_start.html#start_6 for
more details. :l
To change settings for the USER-CUDA package at run-time, the "package
cuda"_package.html command can be used near the beginning of your
@ -388,7 +504,7 @@ 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(acc_5)
Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.

170
doc/Section_commands.html
View File

@ -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>
@ -14,15 +14,15 @@
<P>This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
</P>
3.1 <A HREF = "#3_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#3_2">Parsing rules</A><BR>
3.3 <A HREF = "#3_3">Input script structure</A><BR>
3.4 <A HREF = "#3_4">Commands listed by category</A><BR>
3.5 <A HREF = "#3_5">Commands listed alphabetically</A> <BR>
3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
<HR>
<A NAME = "3_1"></A><H4>3.1 LAMMPS input script
<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
</H4>
<P>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
@ -75,7 +75,7 @@ command lists restrictions on how the command can be used.
</P>
<HR>
<A NAME = "3_2"></A><H4>3.2 Parsing rules
<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
</H4>
<P>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
@ -134,7 +134,7 @@ allowed, but that should be sufficient for most use cases.
</P>
<HR>
<H4><A NAME = "3_3"></A>3.3 Input script structure
<H4><A NAME = "cmd_3"></A>3.3 Input script structure
</H4>
<P>This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
@ -223,11 +223,11 @@ the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
</P>
<HR>
<A NAME = "3_4"></A><H4>3.4 Commands listed by category
<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
</H4>
<P>This section lists all LAMMPS commands, grouped by category. The
<A HREF = "#3_5">next section</A> lists the same commands alphabetically. Note that
some style options for some commands are part of specific LAMMPS
<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
@ -300,12 +300,12 @@ in the command's documentation.
</P>
<HR>
<H4><A NAME = "3_5"></A><A NAME = "comm"></A>3.5 Individual commands
<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
</H4>
<P>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <A HREF = "#3_4">previous
section</A> lists the same commands, grouped by category. Note that
some style options for some commands are part of specific LAMMPS
listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
section</A> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
@ -338,22 +338,25 @@ of each style or click on the style itself for a full description:
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nphug.html">nphug</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
<TR ALIGN="center"><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated fix styles, which can be used if LAMMPS is
@ -361,9 +364,9 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD><TD ><A HREF = "fix_setforce.html">setforce/cuda</A></TD><TD ><A HREF = "fix_shake.html">shake/cuda</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/limit/cuda</A></TD><TD ><A HREF = "fix_viscous.html">viscous/cuda</A>
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb/omp</A></TD><TD ><A HREF = "fix_setforce.html">setforce/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake/cuda</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/limit/cuda</A></TD><TD ><A HREF = "fix_viscous.html">viscous/cuda</A>
</TD></TR></TABLE></DIV>
<HR>
@ -385,11 +388,12 @@ each style or click on the style itself for a full description:
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated compute styles, which can be used if LAMMPS is
@ -409,30 +413,34 @@ potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_brownian.html">brownian</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian/poly</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_edip.html">edip</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_rhosum.html">sph/rhosum</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_taitwater_morris.html">sph/taitwater/morris</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated pair styles, which can be used if LAMMPS is
@ -440,18 +448,35 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_adp.html">adp/omp</A></TD><TD ><A HREF = "pair_airebo.html">airebo/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long/omp</A></TD><TD ><A HREF = "pair_buck_coul.html">buck/coul/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/debye/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_colloid.html">colloid/omp</A></TD><TD ><A HREF = "pair_comb.html">comb/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/debye/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">dipole/cut/omp</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/cd/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_edip.html">edip/omp</A></TD><TD ><A HREF = "pair_eim.html">eim/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gauss.html">gauss/omp</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A> <A HREF = "pair_resquared.html">resquared/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft/omp</A></TD><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A>
</TD></TR></TABLE></DIV>
<HR>
@ -468,7 +493,8 @@ potentials. Click on the style itself for a full description:
</TD></TR></TABLE></DIV>
<P>These are bond styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut</A>
@ -488,7 +514,8 @@ angle potentials. Click on the style itself for a full description:
</TD></TR></TABLE></DIV>
<P>These are angle styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_cmm.html">cg/cmm</A></TD><TD ><A HREF = "angle_cosine_shift.html">cosine/shift</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp</A>
@ -508,12 +535,22 @@ description:
</TD></TR></TABLE></DIV>
<P>These are dihedral styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated dihedral styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls/omp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Improper_style potentials
@ -539,7 +576,8 @@ Kspace solvers. Click on the style itself for a full description:
</TD></TR></TABLE></DIV>
<P>These are Kspace solvers contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/n</A>

163
doc/Section_commands.txt
View File

@ -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)
@ -11,15 +11,15 @@
This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#3_1
3.2 "Parsing rules"_#3_2
3.3 "Input script structure"_#3_3
3.4 "Commands listed by category"_#3_4
3.5 "Commands listed alphabetically"_#3_5 :all(b)
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
3.1 LAMMPS input script :link(3_1),h4
3.1 LAMMPS input script :link(cmd_1),h4
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
@ -72,7 +72,7 @@ command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(3_2),h4
3.2 Parsing rules :link(cmd_2),h4
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
@ -131,7 +131,7 @@ allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(3_3)
3.3 Input script structure :h4,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
@ -220,11 +220,11 @@ the "minimize"_minimize.html command. A parallel tempering
:line
3.4 Commands listed by category :link(3_4),h4
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#3_5 lists the same commands alphabetically. Note that
some style options for some commands are part of specific LAMMPS
"next section"_#cmd_5 lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
@ -297,12 +297,12 @@ Miscellaneous:
:line
3.5 Individual commands :h4,link(3_5),link(comm)
3.5 Individual commands :h4,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#3_4 lists the same commands, grouped by category. Note that
some style options for some commands are part of specific LAMMPS
section"_#cmd_4 lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
@ -418,6 +418,7 @@ of each style or click on the style itself for a full description:
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gravity"_fix_gravity.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
@ -428,6 +429,7 @@ of each style or click on the style itself for a full description:
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph"_fix_nh.html,
"nphug"_fix_nphug.html,
"nph/asphere"_fix_nph_asphere.html,
"nph/sphere"_fix_nph_sphere.html,
"npt"_fix_nh.html,
@ -435,9 +437,12 @@ of each style or click on the style itself for a full description:
"npt/sphere"_fix_npt_sphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.html,
"nvt"_fix_nh.html,
"nvt/asphere"_fix_nvt_asphere.html,
"nvt/sllod"_fix_nvt_sllod.html,
@ -451,6 +456,7 @@ of each style or click on the style itself for a full description:
"qeq/comb"_fix_qeq_comb.html,
"reax/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid"_fix_rigid.html,
"rigid/nve"_fix_rigid.html,
"rigid/nvt"_fix_rigid.html,
@ -479,11 +485,15 @@ of each style or click on the style itself for a full description:
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
These are fix styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"imd"_fix_imd.html,
"langevin/eff"_fix_langevin_eff.html,
"meso"_fix_meso.html,
"meso/stationary"_fix_meso_stationary.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
@ -499,13 +509,15 @@ package"_Section_accelerate.html.
"freeze/cuda"_fix_freeze.html,
"addforce/cuda"_fix_addforce.html,
"addtorque"_fix_addtorque.html,
"aveforce/cuda"_fix_aveforce.html,
"enforce2d/cuda"_fix_enforce2d.html,
"gravity/cuda"_fix_gravity.html,
"gravity/omp"_fix_gravity.html,
"npt/cuda"_fix_nh.html,
"nve/cuda"_fix_nh.html,
"nve/sphere/omp"_fix_nve_sphere.html,
"nvt/cuda"_fix_nh.html,
"qeq/comb/omp"_fix_qeq_comb.html,
"setforce/cuda"_fix_setforce.html,
"shake/cuda"_fix_shake.html,
"temp/berendsen/cuda"_fix_temp_berendsen.html,
@ -569,11 +581,15 @@ each style or click on the style itself for a full description:
"ti"_compute_ti.html :tb(c=6,ea=c)
These are compute styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ackland/atom"_compute_ackland_atom.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"meso_e/atom"_compute_meso_e_atom.html,
"meso_rho/atom"_compute_meso_rho_atom.html,
"meso_t/atom"_compute_meso_t_atom.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
@ -602,6 +618,8 @@ potentials. Click on the style itself for a full description:
"airebo"_pair_airebo.html,
"born"_pair_born.html,
"born/coul/long"_pair_born.html,
"brownian"_pair_brownian.html,
"brownian/poly"_pair_brownian.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
@ -625,6 +643,7 @@ potentials. Click on the style itself for a full description:
"gran/hooke/history"_pair_gran.html,
"hbond/dreiding/lj"_pair_hbond_dreiding.html,
"hbond/dreiding/morse"_pair_hbond_dreiding.html,
"line/lj"_pair_line_lj.html,
"lj/charmm/coul/charmm"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
"lj/charmm/coul/long"_pair_charmm.html,
@ -642,6 +661,9 @@ potentials. Click on the style itself for a full description:
"lj/smooth"_pair_lj_smooth.html,
"lj96/cut"_pair_lj96.html,
"lubricate"_pair_lubricate.html,
"lubricate/poly"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,
"lubricateU/poly"_pair_lubricateU.html,
"meam"_pair_meam.html,
"morse"_pair_morse.html,
"peri/lps"_pair_peri.html,
@ -654,11 +676,13 @@ potentials. Click on the style itself for a full description:
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"tersoff/zbl"_pair_tersoff_zbl.html,
"tri/lj"_pair_tri_lj.html,
"yukawa"_pair_yukawa.html,
"yukawa/colloid"_pair_yukawa_colloid.html :tb(c=4,ea=c)
These are pair styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"awpmd/cut"_pair_awpmd.html,
"buck/coul"_pair_buck_coul.html,
@ -668,63 +692,136 @@ These are pair styles contributed by users, which can be used if
"coul/long/gpu"_pair_coul.html,
"dipole/sf"_pair_dipole.html,
"eam/cd"_pair_eam.html,
"edip"_pair_edip.html,
"eff/cut"_pair_eff.html,
"lj/coul"_pair_lj_coul.html,
"lj/sf"_pair_lj_sf.html,
"reax/c"_pair_reax_c.html :tb(c=4,ea=c)
"reax/c"_pair_reax_c.html,
"sph/heatconduction"_pair_heatconduction.html,
"sph/idealgas"_pair_idealgas.html,
"sph/lj"_pair_lj.html,
"sph/rhosum"_pair_rhosum.html,
"sph/taitwater"_pair_taitwater.html,
"sph/taitwater/morris"_pair_taitwater_morris.html :tb(c=4,ea=c)
These are accelerated pair styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"adp/omp"_pair_adp.html,
"airebo/omp"_pair_airebo.html,
"born/coul/long/cuda"_pair_born.html,
"born/coul/long/omp"_pair_born.html,
"born/omp"_pair_born.html,
"buck/coul/cut/cuda"_pair_buck.html,
"buck/coul/cut/omp"_pair_buck.html,
"buck/coul/long/cuda"_pair_buck.html,
"buck/coul/long/omp"_pair_buck.html,
"buck/coul/omp"_pair_buck_coul.html,
"buck/cuda"_pair_buck.html,
"buck/omp"_pair_buck.html,
"cg/cmm/coul/cut/cuda"_pair_cmm.html,
"cg/cmm/coul/debye/cuda"_pair_cmm.html,
"cg/cmm/coul/long/cuda"_pair_cmm.html,
"cg/cmm/coul/long/gpu"_pair_cmm.html,
"cg/cmm/cuda"_pair_cmm.html,
"cg/cmm/gpu"_pair_cmm.html,
"colloid/omp"_pair_colloid.html,
"comb/omp"_pair_comb.html,
"coul/cut/omp"_pair_coul.html,
"coul/debye/omp"_pair_coul.html,
"coul/long/gpu"_pair_coul.html,
"coul/long/omp"_pair_coul.html,
"dipole/cut/omp"_pair_dipole.html,
"dipole/sf/omp"_pair_dipole.html,
"dpd/omp"_pair_dpd.html,
"dpd/tstat/omp"_pair_dpd.html,
"eam/alloy/cuda"_pair_eam.html,
"eam/alloy/omp"_pair_eam.html,
"eam/alloy/opt"_pair_eam.html,
"eam/cd/omp"_pair_eam.html,
"eam/cuda"_pair_eam.html,
"eam/fs/cuda"_pair_eam.html,
"eam/fs/omp"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"eam/omp"_pair_eam.html,
"eam/opt"_pair_eam.html,
"edip/omp"_pair_edip.html,
"eim/omp"_pair_eim.html,
"gauss/omp"_pair_gauss.html,
"gayberne/gpu"_pair_gayberne.html,
"gayberne/omp"_pair_gayberne.html,
"gran/hertz/history/omp"_pair_gran.html,
"gran/hooke/cuda"_pair_gran.html,
"gran/hooke/history/omp"_pair_gran.html,
"gran/hooke/omp"_pair_gran.html,
"hbond/dreiding/lj/omp"_pair_hbond_dreiding.html,
"hbond/dreiding/morse/omp"_pair_hbond_dreiding.html,
"lj/charmm/coul/charmm/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/omp"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/omp"_pair_charmm.html,
"lj/charmm/coul/long/cuda"_pair_charmm.html,
"lj/charmm/coul/long/gpu"_pair_charmm.html,
"lj/charmm/coul/long/omp"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/class2/coul/cut/cuda"_pair_class2.html,
"lj/class2/coul/cut/omp"_pair_class2.html,
"lj/class2/coul/long/cuda"_pair_class2.html,
"lj/class2/coul/long/gpu"_pair_class2.html,
"lj/class2/coul/long/omp"_pair_class2.html,
"lj/class2/cuda"_pair_class2.html,
"lj/class2/gpu"_pair_class2.html,
"lj/class2/omp"_pair_class2.html,
"lj/coul/omp"_pair_lj_coul.html,
"lj/cut/coul/cut/cuda"_pair_lj.html,
"lj/cut/coul/cut/gpu"_pair_lj.html,
"lj/cut/coul/cut/omp"_pair_lj.html,
"lj/cut/coul/debye/cuda"_pair_lj.html,
"lj/cut/coul/debye/omp"_pair_lj.html,
"lj/cut/coul/long/cuda"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
"lj/cut/coul/long/omp"_pair_lj.html,
"lj/cut/coul/long/opt"_pair_lj.html,
"lj/cut/coul/long/tip4p/omp"_pair_lj.html,
"lj/cut/coul/long/tip4p/opt"_pair_lj.html,
"lj/cut/cuda"_pair_lj.html,
"lj/cut/experimental/cuda"_pair_lj.html,
"lj/cut/gpu"_pair_lj.html,
"lj/cut/omp"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/expand/cuda"_pair_lj_expand.html,
"lj/expand/gpu"_pair_lj_expand.html,
"lj/expand/omp"_pair_lj_expand.html,
"lj/gromacs/coul/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/coul/gromacs/omp"_pair_gromacs.html,
"lj/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/omp"_pair_gromacs.html,
"lj/sf/omp"_pair_lj_sf.html,
"lj/smooth/cuda"_pair_lj_smooth.html,
"lj/smooth/omp"_pair_lj_smooth.html,
"lj96/cut/cuda"_pair_lj96.html,
"lj96/cut/gpu"_pair_lj96.html,
"lj96/cut/omp"_pair_lj96.html,
"lubricate/omp"_pair_lubricate.html,
"morse/cuda"_pair_morse.html,
"morse/gpu"_pair_morse.html,
"morse/omp"_pair_morse.html,
"morse/opt"_pair_morse.html,
"resquared/gpu"_pair_resquared.html :tb(c=4,ea=c)
"peri/lps/omp"_pair_peri.html,
"peri/pmb/omp"_pair_peri.html,
"rebo/omp"_pair_airebo.html,
"resquared/gpu"_pair_resquared.html
"resquared/omp"_pair_resquared.html,
"soft/omp"_pair_soft.html,
"sw/cuda"_pair_sw.html,
"sw/omp"_pair_sw.html,
"table/omp"_pair_table.html,
"tersoff/cuda"_pair_tersoff.html,
"tersoff/omp"_pair_tersoff.html,
"tersoff/zbl/omp"_pair_tersoff_zbl.html,
"yukawa/omp"_pair_yukawa.html,
"yukawa/colloid/omp"_pair_yukawa_colloid.html :tb(c=4,ea=c)
:line
@ -745,7 +842,8 @@ potentials. Click on the style itself for a full description:
"table"_bond_table.html :tb(c=4,ea=c,w=100)
These are bond styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift"_bond_harmonic_shift.html,
"harmonic/shift/cut"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
@ -769,7 +867,8 @@ angle potentials. Click on the style itself for a full description:
"table"_angle_table.html :tb(c=4,ea=c,w=100)
These are angle styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cg/cmm"_angle_cmm.html,
"cosine/shift"_angle_cosine_shift.html,
@ -793,10 +892,23 @@ description:
"opls"_dihedral_opls.html :tb(c=4,ea=c,w=100)
These are dihedral styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp"_dihedral_cosine_shift_exp.html :tb(c=4,ea=c)
These are accelerated dihedral styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"charmm/omp"_dihedral_charmm.html,
"class2/omp"_dihedral_class2.html,
"cosine/shift/exp/omp"_dihedral_cosine_shift_exp.html,
"harmonic/omp"_dihedral_harmonic.html,
"helix/omp"_dihedral_helix.html,
"multi/harmonic/omp"_dihedral_multi_harmonic.html,
"opls/omp"_dihedral_opls.html :tb(c=4,ea=c,w=100)
:line
Improper_style potentials :h4
@ -825,7 +937,8 @@ Kspace solvers. Click on the style itself for a full description:
"pppm/tip4p"_kspace_style.html :tb(c=4,ea=c,w=100)
These are Kspace solvers contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ewald/n"_kspace_style.html :tb(c=4,ea=c,w=100)

32
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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 = "#err_1">Common problems</A><BR>
12.2 <A HREF = "#err_2">Reporting bugs</A><BR>
12.3 <A HREF = "#err_3">Error & warning messages</A> <BR>
<HR>
<A NAME = "11_1"></A><H4>11.1 Common problems
<A NAME = "err_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 = "#err_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 = "err_2"></A><H4>12.2 Reporting bugs
</H4>
<P>If you are confident that you have found a bug in LAMMPS, follow these
steps.
@ -142,18 +142,22 @@ causing the problem.
</P>
<HR>
<H4><A NAME = "11_3"></A>11.3 Error & warning messages
<H4><A NAME = "err_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
explanation here is not sufficient, the documentation for the
offending command may help. Grepping the source files for the text of
the error message and staring at the source code and comments is also
not a bad idea! Note that sometimes the same message can be printed
from multiple places in the code.
offending command may help.
Error and warning messages also list the source file and line number
where the error was generated. For example, this message
</P>
<P>Also note that error messages from <A HREF = "Section_start.html#2_3">user-contributed
packages</A> are not listed here. Is such an
<P>ERROR: Illegal velocity command (velocity.cpp:78)
</P>
<P>means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
</P>
<P>Note that error messages from <A HREF = "Section_start.html#start_3">user-contributed
packages</A> are not listed here. If such an
error occurs and is not self-explanatory, you'll need to look in the
source code or contact the author of the package.
</P>

32
doc/Section_errors.txt
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@ -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"_#err_1
12.2 "Reporting bugs"_#err_2
12.3 "Error & warning messages"_#err_3 :all(b)
:line
11.1 Common problems :link(11_1),h4
12.1 Common problems :link(err_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"_#err_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(err_2),h4
If you are confident that you have found a bug in LAMMPS, follow these
steps.
@ -139,18 +139,22 @@ 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(err_3)
These are two alphabetic lists of the "ERROR"_#error and
"WARNING"_#warn messages LAMMPS prints out and the reason why. If the
explanation here is not sufficient, the documentation for the
offending command may help. Grepping the source files for the text of
the error message and staring at the source code and comments is also
not a bad idea! Note that sometimes the same message can be printed
from multiple places in the code.
offending command may help.
Error and warning messages also list the source file and line number
where the error was generated. For example, this message
Also note that error messages from "user-contributed
packages"_Section_start.html#2_3 are not listed here. Is such an
ERROR: Illegal velocity command (velocity.cpp:78)
means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that error messages from "user-contributed
packages"_Section_start.html#start_3 are not listed here. If such an
error occurs and is not self-explanatory, you'll need to look in the
source code or contact the author of the package.

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

84
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View File

@ -1,5 +1,7 @@
<HTML>
<CENTER><A HREF = "Section_errors.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 = "Manual.html">Next Section</A>
<CENTER><A HREF = "Section_errors.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 = "Manual.html">Next
Section</A>
</CENTER>
@ -9,69 +11,59 @@
<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 = "#hist_1">Coming attractions</A><BR>
13.2 <A HREF = "#hist_2">Past versions</A> <BR>
<HR>
<H4><A NAME = "12_1"></A>12.1 Coming attractions
<H4><A NAME = "hist_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
earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and
GranFlow for granular materials.
<P>The <A HREF = "http://lammps.sandia.gov/future.html">Wish list link</A> on the
LAMMPS WWW page gives a list of features we are hoping to add to
LAMMPS in the future, including contact names of individuals you can
email if you are interested in contributing to the developement or
would be a future user of that feature.
</P>
<P>These are new features we'd like to eventually add to LAMMPS. Some
are being worked on; some haven't been implemented because of lack of
time or interest; others are just a lot of work! See <A HREF = "http://lammps.sandia.gov/future.html">this
page</A> on the LAMMPS WWW site for more details.
<P>You can also send <A HREF = "http://lammps.sandia.gov/authors.html">email to the
developers</A> if you want to add
your wish to the list.
</P>
<UL><LI>Coupling to finite elements for streess-strain
<LI>New ReaxFF implementation
<LI>Nudged elastic band
<LI>Temperature accelerated dynamics
<LI>Triangulated particles
<LI>Stochastic rotation dynamics
<LI>Stokesian dynamics via fast lubrication dynamics
<LI>Long-range point-dipole solver
<LI>Per-atom energy and stress for long-range Coulombics
<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes
<LI>Metadynamics
<LI>Direct Simulation Monte Carlo - DSMC
</UL>
<HR>
<H4><A NAME = "12_2"></A>12.2 Past versions
<H4><A NAME = "hist_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)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). Soon after
the CRADA ended, a final F77 version of the code, LAMMPS 99, was
released. As development of LAMMPS continued at Sandia, the memory
management in the code was converted to F90; a final F90 version was
released as LAMMPS 2001.
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
to develop a large-scale parallel classical MD code; the coding effort
was led by Steve Plimpton at Sandia.
</P>
<P>After the CRADA ended, a final F77 version, LAMMPS 99, was
released. As development of LAMMPS continued at Sandia, its memory
management was converted to F90; a final F90 version was released as
LAMMPS 2001.
</P>
<P>The current LAMMPS is a rewrite in C++ and was first publicly released
in 2004. It includes many new features, including features from other
parallel molecular dynamics codes written at Sandia, namely ParaDyn,
Warp, and GranFlow. ParaDyn is a parallel implementation of the
popular serial DYNAMO code developed by Stephen Foiles and Murray Daw
for their embedded atom method (EAM) metal potentials. ParaDyn uses
atom- and force-decomposition algorithms to run in parallel. Warp is
also a parallel implementation of the EAM potentials designed for
large problems, with boundary conditions specific to shearing solids
in varying geometries. GranFlow is a granular materials code with
potentials and boundary conditions peculiar to granular systems. All
of these codes (except ParaDyn) use spatial-decomposition techniques
for their parallelism.
as an open source code in 2004. It includes many new features beyond
those in LAMMPS 99 or 2001. It also includes features from older
parallel MD codes written at Sandia, namely ParaDyn, Warp, and
GranFlow (see below).
</P>
<P>In late 2006 we began merging new capabilities into LAMMPS that were
developed by Aidan Thompson at Sandia for his MD code GRASP, which has
a parallel framework similar to LAMMPS. Most notably, these have
included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
and the associated charge-equilibration routines needed for ReaxFF.
</P>
<P>The <A HREF = "http://lammps.sandia.gov/history.html">History link</A> on the
LAMMPS WWW page gives a timeline of features added to the
C++ open-source version of LAMMPS over the last several years.
</P>
<P>These older codes are available for download from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
site</A>, except for Warp & GranFlow which were primarily used

84
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@ -1,4 +1,6 @@
"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Manual.html :c
"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Manual.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -6,69 +8,59 @@
: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"_#hist_1
13.2 "Past versions"_#hist_2 :all(b)
:line
12.1 Coming attractions :h4,link(12_1)
13.1 Coming attractions :h4,link(hist_1)
The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes developed at Sandia. These include
earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and
GranFlow for granular materials.
The "Wish list link"_http://lammps.sandia.gov/future.html on the
LAMMPS WWW page gives a list of features we are hoping to add to
LAMMPS in the future, including contact names of individuals you can
email if you are interested in contributing to the developement or
would be a future user of that feature.
These are new features we'd like to eventually add to LAMMPS. Some
are being worked on; some haven't been implemented because of lack of
time or interest; others are just a lot of work! See "this
page"_lwsfuture on the LAMMPS WWW site for more details.
:link(lwsfuture,http://lammps.sandia.gov/future.html)
Coupling to finite elements for streess-strain
New ReaxFF implementation
Nudged elastic band
Temperature accelerated dynamics
Triangulated particles
Stochastic rotation dynamics
Stokesian dynamics via fast lubrication dynamics
Long-range point-dipole solver
Per-atom energy and stress for long-range Coulombics
Long-range Coulombics via Ewald and PPPM for triclinic boxes
Metadynamics
Direct Simulation Monte Carlo - DSMC :ul
You can also send "email to the
developers"_http://lammps.sandia.gov/authors.html if you want to add
your wish to the list.
:line
12.2 Past versions :h4,link(12_2)
13.2 Past versions :h4,link(hist_2)
LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). Soon after
the CRADA ended, a final F77 version of the code, LAMMPS 99, was
released. As development of LAMMPS continued at Sandia, the memory
management in the code was converted to F90; a final F90 version was
released as LAMMPS 2001.
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
to develop a large-scale parallel classical MD code; the coding effort
was led by Steve Plimpton at Sandia.
After the CRADA ended, a final F77 version, LAMMPS 99, was
released. As development of LAMMPS continued at Sandia, its memory
management was converted to F90; a final F90 version was released as
LAMMPS 2001.
The current LAMMPS is a rewrite in C++ and was first publicly released
in 2004. It includes many new features, including features from other
parallel molecular dynamics codes written at Sandia, namely ParaDyn,
Warp, and GranFlow. ParaDyn is a parallel implementation of the
popular serial DYNAMO code developed by Stephen Foiles and Murray Daw
for their embedded atom method (EAM) metal potentials. ParaDyn uses
atom- and force-decomposition algorithms to run in parallel. Warp is
also a parallel implementation of the EAM potentials designed for
large problems, with boundary conditions specific to shearing solids
in varying geometries. GranFlow is a granular materials code with
potentials and boundary conditions peculiar to granular systems. All
of these codes (except ParaDyn) use spatial-decomposition techniques
for their parallelism.
as an open source code in 2004. It includes many new features beyond
those in LAMMPS 99 or 2001. It also includes features from older
parallel MD codes written at Sandia, namely ParaDyn, Warp, and
GranFlow (see below).
In late 2006 we began merging new capabilities into LAMMPS that were
developed by Aidan Thompson at Sandia for his MD code GRASP, which has
a parallel framework similar to LAMMPS. Most notably, these have
included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
and the associated charge-equilibration routines needed for ReaxFF.
The "History link"_http://lammps.sandia.gov/history.html on the
LAMMPS WWW page gives a timeline of features added to the
C++ open-source version of LAMMPS over the last several years.
These older codes are available for download from the "LAMMPS WWW
site"_lws, except for Warp & GranFlow which were primarily used

141
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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 = "#howto_1">Restarting a simulation</A><BR>
6.2 <A HREF = "#howto_2">2d simulations</A><BR>
6.3 <A HREF = "#howto_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
6.4 <A HREF = "#howto_4">Running multiple simulations from one input script</A><BR>
6.5 <A HREF = "#howto_5">Multi-replica simulations</A><BR>
6.6 <A HREF = "#howto_6">Granular models</A><BR>
6.7 <A HREF = "#howto_7">TIP3P water model</A><BR>
6.8 <A HREF = "#howto_8">TIP4P water model</A><BR>
6.9 <A HREF = "#howto_9">SPC water model</A><BR>
6.10 <A HREF = "#howto_10">Coupling LAMMPS to other codes</A><BR>
6.11 <A HREF = "#howto_11">Visualizing LAMMPS snapshots</A><BR>
6.12 <A HREF = "#howto_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
6.13 <A HREF = "#howto_13">NEMD simulations</A><BR>
6.14 <A HREF = "#howto_14">Extended spherical and aspherical particles</A><BR>
6.15 <A HREF = "#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
6.16 <A HREF = "#howto_16">Thermostatting, barostatting and computing temperature</A><BR>
6.17 <A HREF = "#howto_17">Walls</A><BR>
6.18 <A HREF = "#howto_18">Elastic constants</A><BR>
6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
6.21 <A HREF = "#howto_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 = "howto_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 = "howto_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 = "howto_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 = "howto_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.
@ -318,7 +318,7 @@ jump in.polymer
<P>All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in <A HREF = "Section_start.html#2_6">this
the "-partition" command-line switch as described in <A HREF = "Section_start.html#start_6">this
section</A> of the manual.
</P>
<P>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
@ -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 = "howto_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
@ -355,12 +355,12 @@ runs different replicas at a series of temperature to facilitate
rare-event sampling.
</P>
<P>These command can only be used if LAMMPS was built with the "replica"
package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
more info on packages.
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P>In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the <A HREF = "Section_start.html#2_6">-partition command-line
run-time by using the <A HREF = "Section_start.html#start_6">-partition command-line
switch</A> to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
@ -369,8 +369,8 @@ these commands:
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
</PRE>
<P>would each run 8 replicas, on either 16 or 8 processors. Note the use
of the <A HREF = "Section_start.html#2_6">-in command-line switch</A> to specify the
input script which is required when running in multi-replica mode.
of the <A HREF = "Section_start.html#start_6">-in command-line switch</A> to specify
the input script which is required when running in multi-replica mode.
</P>
<P>Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
@ -381,7 +381,7 @@ physical processors.
</P>
<HR>
<A NAME = "4_6"></A><H4>4.6 Granular models
<A NAME = "howto_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#howto_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 = "howto_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 = "howto_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 = "howto_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 = "howto_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
@ -660,10 +660,10 @@ strain induced across grain boundaries
<P><A HREF = "Section_start.html#2_4">This section</A> of the documentation describes
how to build LAMMPS as a library. Once this is done, you can
interface with LAMMPS either via C++, C, Fortran, or Python (or any
other language that supports a vanilla C-like interface). For
<P><A HREF = "Section_start.html#start_4">This section</A> of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) "instances" of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
@ -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#howto_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 = "howto_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 = "howto_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 = "howto_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 = "howto_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 = "howto_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 = "howto_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 = "#howto_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 = "howto_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 = "howto_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
@ -1655,12 +1655,12 @@ 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 = "howto_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
through a <A HREF = "Section_python.html">Python interface</A>.
<P>As described in <A HREF = "Section_start.html#start_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#howto_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
provided in the files src/library.cpp and src/library.h. The
@ -1679,11 +1679,12 @@ void lammps_file(void *, char *);
char *lammps_command(void *, char *);
</PRE>
<P>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <A HREF = "#2_6">command-line arguments</A> when
LAMMPS is run in stand-alone mode from the command line, and a MPI
communicator for LAMMPS to run under. It returns a ptr to the LAMMPS
object that is created, and which is used in subsequent library calls.
The lammps_open() function can be called multiple times, to create
list of strings as if they were <A HREF = "Section_start.html#start_6">command-line
arguments</A> when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.
</P>
<P>LAMMPS will run on the set of processors in the communicator. This
@ -1735,10 +1736,10 @@ 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 = "howto_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#howto_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 +1756,7 @@ 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#howto_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 +1801,10 @@ formalism.
</P>
<HR>
<A NAME = "4_21"></A><H4>4.21 Calculating viscosity
<A NAME = "howto_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#howto_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 +1830,7 @@ 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#howto_13">this
section</A> of the manual for details on NEMD
simulations.
</P>

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@ -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"_#howto_1
6.2 "2d simulations"_#howto_2
6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3
6.4 "Running multiple simulations from one input script"_#howto_4
6.5 "Multi-replica simulations"_#howto_5
6.6 "Granular models"_#howto_6
6.7 "TIP3P water model"_#howto_7
6.8 "TIP4P water model"_#howto_8
6.9 "SPC water model"_#howto_9
6.10 "Coupling LAMMPS to other codes"_#howto_10
6.11 "Visualizing LAMMPS snapshots"_#howto_11
6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
6.13 "NEMD simulations"_#howto_13
6.14 "Extended spherical and aspherical particles"_#howto_14
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
6.17 "Walls"_#howto_17
6.18 "Elastic constants"_#howto_18
6.19 "Library interface to LAMMPS"_#howto_19
6.20 "Calculating thermal conductivity"_#howto_20
6.21 "Calculating viscosity"_#howto_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(howto_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(howto_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(howto_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(howto_4),h4
This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
@ -315,7 +315,7 @@ All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in "this
section"_Section_start.html#2_6 of the manual.
section"_Section_start.html#start_6 of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
@ -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(howto_5),h4
Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
@ -351,13 +351,13 @@ runs different replicas at a series of temperature to facilitate
rare-event sampling.
These command can only be used if LAMMPS was built with the "replica"
package. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info on packages.
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
switch"_Section_start.html#2_6 to launch LAMMPS on multiple
switch"_Section_start.html#start_6 to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
@ -365,8 +365,8 @@ mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
of the "-in command-line switch"_Section_start.html#2_6 to specify the
input script which is required when running in multi-replica mode.
of the "-in command-line switch"_Section_start.html#start_6 to specify
the input script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
@ -377,7 +377,7 @@ physical processors.
:line
4.6 Granular models :link(4_6),h4
6.6 Granular models :link(howto_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#howto_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(howto_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(howto_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(howto_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(howto_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
@ -655,10 +655,10 @@ strain induced across grain boundaries :l,ule
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
"This section"_Section_start.html#2_4 of the documentation describes
how to build LAMMPS as a library. Once this is done, you can
interface with LAMMPS either via C++, C, Fortran, or Python (or any
other language that supports a vanilla C-like interface). For
"This section"_Section_start.html#start_4 of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) "instances" of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
@ -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#howto_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(howto_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(howto_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(howto_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(howto_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(howto_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(howto_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"_#howto_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(howto_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(howto_18),h4
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
@ -1643,12 +1643,12 @@ 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(howto_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
through a "Python interface"_Section_python.html.
As described in "this section"_Section_start.html#start_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#howto_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
provided in the files src/library.cpp and src/library.h. The
@ -1667,11 +1667,12 @@ void lammps_file(void *, char *);
char *lammps_command(void *, char *); :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line arguments"_#2_6 when
LAMMPS is run in stand-alone mode from the command line, and a MPI
communicator for LAMMPS to run under. It returns a ptr to the LAMMPS
object that is created, and which is used in subsequent library calls.
The lammps_open() function can be called multiple times, to create
list of strings as if they were "command-line
arguments"_Section_start.html#start_6 when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
@ -1723,11 +1724,11 @@ 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(howto_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#howto_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 +1744,7 @@ 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#howto_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 +1789,11 @@ formalism.
:line
4.21 Calculating viscosity :link(4_21),h4
6.21 Calculating viscosity :link(howto_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#howto_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 +1819,7 @@ 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#howto_13 of the manual for details on NEMD
simulations.
The second method is to perform a reverse non-equilibrium MD

220
doc/Section_intro.html
View File

@ -16,15 +16,15 @@ describe what it means for LAMMPS to be an open-source code, and
acknowledge the funding and people who have contributed to LAMMPS over
the years.
</P>
1.1 <A HREF = "#1_1">What is LAMMPS</A><BR>
1.2 <A HREF = "#1_2">LAMMPS features</A><BR>
1.3 <A HREF = "#1_3">LAMMPS non-features</A><BR>
1.4 <A HREF = "#1_4">Open source distribution</A><BR>
1.5 <A HREF = "#1_5">Acknowledgments and citations</A> <BR>
1.1 <A HREF = "#intro_1">What is LAMMPS</A><BR>
1.2 <A HREF = "#intro_2">LAMMPS features</A><BR>
1.3 <A HREF = "#intro_3">LAMMPS non-features</A><BR>
1.4 <A HREF = "#intro_4">Open source distribution</A><BR>
1.5 <A HREF = "#intro_5">Acknowledgments and citations</A> <BR>
<HR>
<A NAME = "1_1"></A><H4>1.1 What is LAMMPS
<A NAME = "intro_1"></A><H4>1.1 What is LAMMPS
</H4>
<P>LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
@ -49,7 +49,7 @@ WWW Site</A>.
</P>
<P>LAMMPS is a freely-available open-source code, distributed under the
terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A>, which means you can use or
modify the code however you wish. See <A HREF = "#1_4">this section</A> for a brief
modify the code however you wish. See <A HREF = "#intro_4">this section</A> for a brief
discussion of the open-source philosophy.
</P>
@ -67,7 +67,7 @@ downloaded from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
<P>LAMMPS was originally developed under a US Department of Energy CRADA
(Cooperative Research and Development Agreement) between two DOE labs
and 3 companies. It is distributed by <A HREF = "http://www.sandia.gov">Sandia National Labs</A>.
See <A HREF = "#1_5">this section</A> for more information on LAMMPS funding and
See <A HREF = "#intro_5">this section</A> for more information on LAMMPS funding and
individuals who have contributed to LAMMPS.
</P>
@ -86,11 +86,11 @@ communicate and store "ghost" atom information for atoms that border
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
systems whose particles fill a 3d rectangular box with roughly uniform
density. Papers with technical details of the algorithms used in
LAMMPS are listed in <A HREF = "#1_5">this section</A>.
LAMMPS are listed in <A HREF = "#intro_5">this section</A>.
</P>
<HR>
<A NAME = "1_2"></A><H4>1.2 LAMMPS features
<A NAME = "intro_2"></A><H4>1.2 LAMMPS features
</H4>
<P>This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
@ -125,7 +125,8 @@ LAMMPS.
<LI> metals
<LI> granular materials
<LI> coarse-grained mesoscale models
<LI> extended spherical and ellipsoidal particles
<LI> finite-size spherical and ellipsoidal particles
<LI> finite-size line segment (2d) and triangle (3d) particles
<LI> point dipolar particles
<LI> rigid collections of particles
<LI> hybrid combinations of these
@ -139,10 +140,10 @@ commands)
</P>
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
<LI> charged pairwise potentials: Coulombic, point-dipole
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
<LI> electron force field (eFF, AWPMD)
<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
<LI> mesoscopic potentials: granular, Peridynamics
<LI> mesoscopic potentials: granular, Peridynamics, SPH
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS)
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
@ -246,6 +247,7 @@ molecular dynamics options:
<LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
<LI><A HREF = "doc/fix_gcmc.html">grand canonical Monte Carlo</A> insertions/deletions
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
@ -253,7 +255,7 @@ molecular dynamics options:
</UL>
<HR>
<A NAME = "1_3"></A><H4>1.3 LAMMPS non-features
<A NAME = "intro_3"></A><H4>1.3 LAMMPS non-features
</H4>
<P>LAMMPS is designed to efficiently compute Newton's equations of motion
for a system of interacting particles. Many of the tools needed to
@ -371,7 +373,7 @@ spatial-decomposition version exist.
</P>
<HR>
<A NAME = "1_4"></A><H4>1.4 Open source distribution
<A NAME = "intro_4"></A><H4>1.4 Open source distribution
</H4>
<P>LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
@ -416,7 +418,7 @@ Site</A>, or have a suggestion for something to clarify or include,
send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
<LI>If you find a bug, <A HREF = "Section_errors.html#10_2">this section</A> describes
<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
how to report it.
<LI>If you publish a paper using LAMMPS results, send the citation (and
@ -454,7 +456,7 @@ encouraged.
</UL>
<HR>
<H4><A NAME = "1_5"></A>1.5 Acknowledgments and citations
<H4><A NAME = "intro_5"></A>1.5 Acknowledgments and citations
</H4>
<P>LAMMPS development has been funded by the <A HREF = "http://www.doe.gov">US Department of
Energy</A> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
@ -476,154 +478,58 @@ Hierarchical Modeling".
<P>The following papers describe the parallel algorithms used in LAMMPS.
<P>The following paper describe the basic parallel algorithms used in
LAMMPS. If you use LAMMPS results in your published work, please cite
this paper and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov):
</P>
<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
</P>
<P>S. J. Plimpton, R. Pollock, M. Stevens, <B>Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations</B>, in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
<P>Other papers describing specific algorithms used in LAMMPS are listed
under the <A HREF = "http://lammps.sandia.gov/cite.html">Citing LAMMPS link</A> of
the LAMMPS WWW page.
</P>
<P>If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov).
<P>The <A HREF = "http://lammps.sandia.gov/papers.html">Publications link</A> on the
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
not listed there for some reason, feel free to send us the info. If
the simulations in your paper produced cool pictures or animations,
we'll be pleased to add them to the
<A HREF = "http://lammps.sandia.gov/pictures.html">Pictures</A> or
<A HREF = "http://lammps.sandia.gov/movies.html">Movies</A> pages of the LAMMPS WWW
site.
</P>
<P>If you send is information about your publication, we'll be pleased to
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
for a picture or movie for the Pictures or Movies pages.
<P>The core group of LAMMPS developers is at Sandia National Labs:
</P>
<P>The core group of LAMMPS developers is at Sandia National Labs. They
include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
<UL><LI>Steve Plimpton, sjplimp at sandia.gov
<LI>Aidan Thompson, athomps at sandia.gov
<LI>Paul Crozier, pscrozi at sandia.gov
</UL>
<P>The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
</P>
<P>Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >pppm GPU single and double </TD><TD > Mike Brown (ORNL)</TD></TR>
<TR><TD >pair_style lj/cut/expand </TD><TD > Inderaj Bains (NVIDIA)</TD></TR>
<TR><TD >temperature accelerated dynamics (TAD) </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >pair reax/c and fix qeq/reax </TD><TD > Metin Aktulga (Purdue, now LBNL)</TD></TR>
<TR><TD >DREIDING force field, pair_style hbond/dreiding, etc </TD><TD > Tod Pascal (CalTech)</TD></TR>
<TR><TD >fix adapt and compute ti for thermodynamic integreation for free energies </TD><TD > Sai Jayaraman (Sandia)</TD></TR>
<TR><TD >pair born and pair gauss </TD><TD > Sai Jayaraman (Sandia)</TD></TR>
<TR><TD >stochastic rotation dynamics (SRD) via fix srd </TD><TD > Jemery Lechman (Sandia) and Pieter in 't Veld (BASF)</TD></TR>
<TR><TD >ipp Perl script tool </TD><TD > Reese Jones (Sandia)</TD></TR>
<TR><TD >eam_database and createatoms tools </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >electron force field (eFF) </TD><TD > Andres Jaramillo-Botero and Julius Su (Caltech)</TD></TR>
<TR><TD >embedded ion method (EIM) potential </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >COMB potential with charge equilibration </TD><TD > Tzu-Ray Shan (U Florida)</TD></TR>
<TR><TD >fix ave/correlate </TD><TD > Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)</TD></TR>
<TR><TD >pair_style peri/lps </TD><TD > Mike Parks (Sandia)</TD></TR>
<TR><TD >fix msst </TD><TD > Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)</TD></TR>
<TR><TD >thermo_style custom tpcpu & spcpu keywords </TD><TD > Axel Kohlmeyer (Temple U) </TD></TR>
<TR><TD >fix rigid/nve, fix rigid/nvt </TD><TD > Tony Sheh and Trung Dac Nguyen (U Michigan)</TD></TR>
<TR><TD >public SVN & Git repositories for LAMMPS </TD><TD > Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)</TD></TR>
<TR><TD >fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >compute heat/flux </TD><TD > German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)</TD></TR>
<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>
<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>
<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>
<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>
<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>
<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>
<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >pair born/coul/long </TD><TD > Ahmed Ismail (Sandia)</TD></TR>
<TR><TD >fix ttm </TD><TD > Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)</TD></TR>
<TR><TD >fix box/relax </TD><TD > Aidan Thompson and David Olmsted (Sandia)</TD></TR>
<TR><TD >ReaxFF potential </TD><TD > Aidan Thompson (Sandia) and Hansohl Cho (MIT)</TD></TR>
<TR><TD >compute cna/atom </TD><TD > Wan Liang (Chinese Academy of Sciences)</TD></TR>
<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >compute group/group </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >CG-CMM user package for coarse-graining </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >cosine/delta angle potential </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >VIM editor add-ons for LAMMPS input scripts </TD><TD > Gerolf Ziegenhain</TD></TR>
<TR><TD >pair lubricate </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >compute ackland/atom </TD><TD > Gerolf Zeigenhain</TD></TR>
<TR><TD >kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >AIREBO bond-order potential </TD><TD > Ase Henry (MIT)</TD></TR>
<TR><TD >making LAMMPS a true "object" that can be instantiated multiple times, e.g. as a library </TD><TD > Ben FrantzDale (RPI)</TD></TR>
<TR><TD >pymol_asphere viz tool </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >NEMD SLLOD integration </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >tensile and shear deformations </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >GayBerne potential </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >ellipsoidal particles </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >colloid potentials </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >fix heat </TD><TD > Paul Crozier and Ed Webb (Sandia)</TD></TR>
<TR><TD >neighbor multi and communicate multi </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >MATLAB post-processing scripts </TD><TD > Arun Subramaniyan (Purdue)</TD></TR>
<TR><TD >triclinic (non-orthogonal) simulation domains </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >thermo_extract tool</TD><TD > Vikas Varshney (Wright Patterson AFB)</TD></TR>
<TR><TD >fix ave/time and fix ave/spatial </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >MEAM potential </TD><TD > Greg Wagner (Sandia)</TD></TR>
<TR><TD >optimized pair potentials for lj/cut, charmm/long, eam, morse </TD><TD > James Fischer (High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies)</TD></TR>
<TR><TD >fix wall/lj126 </TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >Stillinger-Weber and Tersoff potentials </TD><TD > Aidan Thompson and Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >region prism </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >LJ tail corrections for energy/pressure </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >fix momentum and recenter </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >multi-letter variable names </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >OPLS dihedral potential</TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >POEMS coupled rigid body integrator</TD><TD > Rudranarayan Mukherjee (RPI)</TD></TR>
<TR><TD >faster pair hybrid potential</TD><TD > James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)</TD></TR>
<TR><TD >breakable bond quartic potential</TD><TD > Chris Lorenz and Mark Stevens (Sandia)</TD></TR>
<TR><TD >DCD and XTC dump styles</TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >grain boundary orientation fix </TD><TD > Koenraad Janssens and David Olmsted (Sandia)</TD></TR>
<TR><TD >lj/smooth pair potential </TD><TD > Craig Maloney (UCSB) </TD></TR>
<TR><TD >radius-of-gyration spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia)</TD></TR>
<TR><TD >self spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >EAM CoAl and AlCu potentials </TD><TD > Kwang-Reoul Lee (KIST, Korea)</TD></TR>
<TR><TD >cosine/squared angle potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >helix dihedral potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia)</TD></TR>
<TR><TD >Finnis/Sinclair EAM</TD><TD > Tim Lau (MIT)</TD></TR>
<TR><TD >dissipative particle dynamics (DPD) potentials</TD><TD > Kurt Smith (U Pitt) and Frank van Swol (Sandia)</TD></TR>
<TR><TD >TIP4P potential (4-site water)</TD><TD > Ahmed Ismail and Amalie Frischknecht (Sandia)</TD></TR>
<TR><TD >uniaxial strain fix</TD><TD > Carsten Svaneborg (Max Planck Institute)</TD></TR>
<TR><TD >thermodynamics enhanced by fix quantities</TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >compressed dump files</TD><TD > Erik Luijten (U Illinois)</TD></TR>
<TR><TD >cylindrical indenter fix</TD><TD > Ravi Agrawal (Northwestern U)</TD></TR>
<TR><TD >electric field fix</TD><TD > Christina Payne (Vanderbilt U)</TD></TR>
<TR><TD >AMBER <-> LAMMPS tool</TD><TD > Keir Novik (Univ College London) and Vikas Varshney (U Akron)</TD></TR>
<TR><TD >CHARMM <-> LAMMPS tool</TD><TD > Pieter in 't Veld and Paul Crozier (Sandia)</TD></TR>
<TR><TD >Morse bond potential</TD><TD > Jeff Greathouse (Sandia)</TD></TR>
<TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR>
<TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)</TD></TR>
<TR><TD >FFT support for SGI SCSL (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
<TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR>
<TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR>
<TR><TD >embedded atom method (EAM) potential</TD><TD > Stephen Foiles (Sandia)</TD></TR>
<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Puetz (Sandia)</TD></TR>
<TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR>
<TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >msi2lmp tool</TD><TD > Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)</TD></TR>
<TR><TD >HTFN energy minimizer</TD><TD > Todd Plantenga (Sandia)</TD></TR>
<TR><TD >class 2 force fields</TD><TD > Eric Simon (Cray)</TD></TR>
<TR><TD >NVT/NPT integrators</TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >rRESPA</TD><TD > Mark Stevens & Paul Crozier (Sandia)</TD></TR>
<TR><TD >Ewald and PPPM solvers</TD><TD > Roy Pollock (LLNL) </TD><TD >
</TD></TR></TABLE></DIV>
<P>Other CRADA partners involved in the design and testing of LAMMPS were
<UL><LI>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
<LI>Roy Pollock (LLNL), Ewald and PPPM solvers
<LI>Mike Brown (ORNL), brownw at ornl.gov, GPU package
<LI>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
<LI>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
<LI>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
<LI>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
<LI>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
<LI>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
<LI>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
<LI>Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
<LI>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
<LI>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
<LI>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package
</UL>
<P>As discussed in <A HREF = "Section_history.html">this section</A>, LAMMPS originated
as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
</P>
<UL><LI>John Carpenter (Mayo Clinic, formerly at Cray Research)
<LI>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)

226
doc/Section_intro.txt
View File

@ -13,15 +13,15 @@ describe what it means for LAMMPS to be an open-source code, and
acknowledge the funding and people who have contributed to LAMMPS over
the years.
1.1 "What is LAMMPS"_#1_1
1.2 "LAMMPS features"_#1_2
1.3 "LAMMPS non-features"_#1_3
1.4 "Open source distribution"_#1_4
1.5 "Acknowledgments and citations"_#1_5 :all(b)
1.1 "What is LAMMPS"_#intro_1
1.2 "LAMMPS features"_#intro_2
1.3 "LAMMPS non-features"_#intro_3
1.4 "Open source distribution"_#intro_4
1.5 "Acknowledgments and citations"_#intro_5 :all(b)
:line
1.1 What is LAMMPS :link(1_1),h4
1.1 What is LAMMPS :link(intro_1),h4
LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
@ -46,7 +46,7 @@ WWW Site"_lws.
LAMMPS is a freely-available open-source code, distributed under the
terms of the "GNU Public License"_gnu, which means you can use or
modify the code however you wish. See "this section"_#1_4 for a brief
modify the code however you wish. See "this section"_#intro_4 for a brief
discussion of the open-source philosophy.
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
@ -64,7 +64,7 @@ downloaded from the "LAMMPS WWW Site"_lws.
LAMMPS was originally developed under a US Department of Energy CRADA
(Cooperative Research and Development Agreement) between two DOE labs
and 3 companies. It is distributed by "Sandia National Labs"_snl.
See "this section"_#1_5 for more information on LAMMPS funding and
See "this section"_#intro_5 for more information on LAMMPS funding and
individuals who have contributed to LAMMPS.
:link(snl,http://www.sandia.gov)
@ -83,11 +83,11 @@ communicate and store "ghost" atom information for atoms that border
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
systems whose particles fill a 3d rectangular box with roughly uniform
density. Papers with technical details of the algorithms used in
LAMMPS are listed in "this section"_#1_5.
LAMMPS are listed in "this section"_#intro_5.
:line
1.2 LAMMPS features :link(1_2),h4
1.2 LAMMPS features :link(intro_2),h4
This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
@ -121,7 +121,8 @@ Particle and model types :h4
metals
granular materials
coarse-grained mesoscale models
extended spherical and ellipsoidal particles
finite-size spherical and ellipsoidal particles
finite-size line segment (2d) and triangle (3d) particles
point dipolar particles
rigid collections of particles
hybrid combinations of these :ul
@ -136,10 +137,10 @@ commands)
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
embedded ion method (EIM), ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
electron force field (eFF, AWPMD)
coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
mesoscopic potentials: granular, Peridynamics
mesoscopic potentials: granular, Peridynamics, SPH
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
@ -242,6 +243,7 @@ molecular dynamics options:
"real-time visualization and interactive MD"_fix_imd.html
"atom-to-continuum coupling"_fix_atc.html with finite elements
coupled rigid body integration via the "POEMS"_fix_poems.html library
"grand canonical Monte Carlo"_doc/fix_gcmc.html insertions/deletions
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
"Peridynamics mesoscale modeling"_pair_peri.html
"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
@ -249,7 +251,7 @@ coupled rigid body integration via the "POEMS"_fix_poems.html library
:line
1.3 LAMMPS non-features :link(1_3),h4
1.3 LAMMPS non-features :link(intro_3),h4
LAMMPS is designed to efficiently compute Newton's equations of motion
for a system of interacting particles. Many of the tools needed to
@ -362,7 +364,7 @@ spatial-decomposition version exist.
:line
1.4 Open source distribution :link(1_4),h4
1.4 Open source distribution :link(intro_4),h4
LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
@ -406,7 +408,7 @@ Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, "this section"_Section_errors.html#10_2 describes
If you find a bug, "this section"_Section_errors.html#err_2 describes
how to report it. :l
If you publish a paper using LAMMPS results, send the citation (and
@ -444,7 +446,7 @@ encouraged. :ule,l
:line
1.5 Acknowledgments and citations :h4,link(1_5)
1.5 Acknowledgments and citations :h4,link(intro_5)
LAMMPS development has been funded by the "US Department of
Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
@ -462,165 +464,59 @@ Hierarchical Modeling".
:link(oascr,http://www.sc.doe.gov/ascr/home.html)
:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
The following papers describe the parallel algorithms used in LAMMPS.
The following paper describe the basic parallel algorithms used in
LAMMPS. If you use LAMMPS results in your published work, please cite
this paper and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov):
S. J. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
Dynamics], J Comp Phys, 117, 1-19 (1995).
S. J. Plimpton, R. Pollock, M. Stevens, [Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations], in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
Other papers describing specific algorithms used in LAMMPS are listed
under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
the LAMMPS WWW page.
If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov).
The "Publications link"_http://lammps.sandia.gov/papers.html on the
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
not listed there for some reason, feel free to send us the info. If
the simulations in your paper produced cool pictures or animations,
we'll be pleased to add them to the
"Pictures"_http://lammps.sandia.gov/pictures.html or
"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
site.
If you send is information about your publication, we'll be pleased to
add it to the Publications page of the "LAMMPS WWW Site"_lws. Ditto
for a picture or movie for the Pictures or Movies pages.
The core group of LAMMPS developers is at Sandia National Labs:
The core group of LAMMPS developers is at Sandia National Labs. They
include "Steve Plimpton"_sjp, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
Steve Plimpton, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Paul Crozier, pscrozi at sandia.gov :ul
Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
:link(sjp,http://www.sandia.gov/~sjplimp)
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul
pppm GPU single and double : Mike Brown (ORNL)
pair_style lj/cut/expand : Inderaj Bains (NVIDIA)
temperature accelerated dynamics (TAD) : Aidan Thompson (Sandia)
pair reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (CalTech)
fix adapt and compute ti for thermodynamic integreation for free energies : Sai Jayaraman (Sandia)
pair born and pair gauss : Sai Jayaraman (Sandia)
stochastic rotation dynamics (SRD) via fix srd : Jemery Lechman (Sandia) and Pieter in 't Veld (BASF)
ipp Perl script tool : Reese Jones (Sandia)
eam_database and createatoms tools : Xiaowang Zhou (Sandia)
electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
fix ave/correlate : Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)
pair_style peri/lps : Mike Parks (Sandia)
fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
public SVN & Git repositories for LAMMPS : Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax : Aidan Thompson (Sandia)
compute heat/flux : German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)
pair yukawa/colloid : Randy Schunk (Sandia)
fix wall/colloid : Jeremy Lechman (Sandia)
pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia)
fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
concentration-dependent EAM potential : Alexander Stukowski (Technical University of Darmstadt)
parallel replica dymamics (PRD) : Mike Brown (Sandia)
min_style hftn : Todd Plantenga (Sandia)
fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
dump cfg : Liang Wan (Chinese Academy of Sciences)
fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
fix langevin tally : Carolyn Phillips (U Michigan)
compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
region cone : Pim Schravendijk
fix reax/bonds : Aidan Thompson (Sandia)
pair born/coul/long : Ahmed Ismail (Sandia)
fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
fix box/relax : Aidan Thompson and David Olmsted (Sandia)
ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
compute cna/atom : Wan Liang (Chinese Academy of Sciences)
Tersoff/ZBL potential : Dave Farrell (Northwestern U)
peridynamics : Mike Parks (Sandia)
fix smd for steered MD : Axel Kohlmeyer (U Penn)
GROMACS pair potentials : Mark Stevens (Sandia)
lmp2vmd tool : Axel Kohlmeyer (U Penn)
compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
CG-CMM user package for coarse-graining : Axel Kohlmeyer (U Penn)
cosine/delta angle potential : Axel Kohlmeyer (U Penn)
VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
pair lubricate : Randy Schunk (Sandia)
compute ackland/atom : Gerolf Zeigenhain
kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
Pieter in 't Veld (Sandia)
AIREBO bond-order potential : Ase Henry (MIT)
making LAMMPS a true "object" that can be instantiated multiple times, \
e.g. as a library : Ben FrantzDale (RPI)
pymol_asphere viz tool : Mike Brown (Sandia)
NEMD SLLOD integration : Pieter in 't Veld (Sandia)
tensile and shear deformations : Pieter in 't Veld (Sandia)
GayBerne potential : Mike Brown (Sandia)
ellipsoidal particles : Mike Brown (Sandia)
colloid potentials : Pieter in 't Veld (Sandia)
fix heat : Paul Crozier and Ed Webb (Sandia)
neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
MEAM potential : Greg Wagner (Sandia)
optimized pair potentials for lj/cut, charmm/long, eam, morse : \
James Fischer (High Performance Technologies), \
David Richie and Vincent Natoli (Stone Ridge Technologies)
fix wall/lj126 : Mark Stevens (Sandia)
Stillinger-Weber and Tersoff potentials : Aidan Thompson and Xiaowang Zhou (Sandia)
region prism : Pieter in 't Veld (Sandia)
LJ tail corrections for energy/pressure : Paul Crozier (Sandia)
fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
OPLS dihedral potential: Mark Stevens (Sandia)
POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
faster pair hybrid potential: James Fischer \
(High Performance Technologies, Inc), Vincent Natoli and \
David Richie (Stone Ridge Technology)
breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
grain boundary orientation fix : Koenraad Janssens and David Olmsted (Sandia)
lj/smooth pair potential : Craig Maloney (UCSB)
radius-of-gyration spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Paul Crozier (Sandia)
self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Mark Stevens (Sandia)
Finnis/Sinclair EAM: Tim Lau (MIT)
dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
Frank van Swol (Sandia)
TIP4P potential (4-site water): Ahmed Ismail and Amalie Frischknecht (Sandia)
uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
thermodynamics enhanced by fix quantities: Aidan Thompson (Sandia)
compressed dump files: Erik Luijten (U Illinois)
cylindrical indenter fix: Ravi Agrawal (Northwestern U)
electric field fix: Christina Payne (Vanderbilt U)
AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
Vikas Varshney (U Akron)
CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
Morse bond potential: Jeff Greathouse (Sandia)
radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
force tables for long-range Coulombics: Paul Crozier (Sandia)
targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
Christian Burisch (Bochum University, Germany)
FFT support for SGI SCSL (Altix): Jim Shepherd (Ga Tech)
lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
Andrey Kalinichev (Sandia)
parallel tempering: Mark Sears (Sandia)
embedded atom method (EAM) potential: Stephen Foiles (Sandia)
multi-harmonic dihedral potential: Mathias Puetz (Sandia)
granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
2d Ewald/PPPM: Paul Crozier (Sandia)
CHARMM force fields: Paul Crozier (Sandia)
msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
HTFN energy minimizer: Todd Plantenga (Sandia)
class 2 force fields: Eric Simon (Cray)
NVT/NPT integrators: Mark Stevens (Sandia)
rRESPA: Mark Stevens & Paul Crozier (Sandia)
Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:)
As discussed in "this section"_Section_history.html, LAMMPS originated
as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
Other CRADA partners involved in the design and testing of LAMMPS were
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)

298
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
@ -22,7 +22,7 @@ with minimal instructions. If you add a new feature to LAMMPS and
think it will be of interest to general users, we encourage you to
submit it to the developers for inclusion in the released version of
LAMMPS. Information about how to do this is provided
<A HREF = "#package">below</A>.
<A HREF = "#mod_14">below</A>.
</P>
<P>The best way to add a new feature is to find a similar feature in
LAMMPS and look at the corresponding source and header files to figure
@ -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
@ -136,52 +113,78 @@ 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 = "#mod_1">Atom styles</A><BR>
10.2 <A HREF = "#mod_2">Bond, angle, dihedral, improper potentials</A><BR>
10.3 <A HREF = "#mod_3">Compute styles</A><BR>
10.4 <A HREF = "#mod_4">Dump styles</A><BR>
10.5 <A HREF = "#mod_5">Dump custom output options</A><BR>
10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
10.7 <A HREF = "mod_7">Input script commands</A><BR>
10.8 <A HREF = "#mod_8">Kspace computations</A><BR>
10.9 <A HREF = "#mod_9">Minimization styles</A><BR>
10.10 <A HREF = "#mod_10">Pairwise potentials</A><BR>
10.11 <A HREF = "#mod_11">Region styles</A><BR>
10.12 <A HREF = "#mod_12">Thermodynamic output options</A><BR>
10.13 <A HREF = "#mod_13">Variable options</A><BR>
10.14 <A HREF = "#mod_14">Submitting new features for inclusion in LAMMPS</A> <BR>
<HR>
<A NAME = "atom"></A><H4>Atom styles
<HR>
<A NAME = "mod_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.
A new atom style can be created if one of the existing atom styles
does not define all the arrays you need to store and communicate with
atoms.
<P>Classes that define an atom style are derived from the AtomVec class
and managed by the Atom class. The atom style determines what
quantities are associated with an atom. A new atom style can be
created if one of the existing atom styles does not define all
the arrays you need to store and communicate with atoms.
</P>
<P>Atom_vec_atomic.cpp is a simple example of an atom style.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See atom.h for details.
class. See atom_vec.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths</TD></TR>
<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations</TD></TR>
<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep</TD></TR>
<TR><TD >pack_comm_vel</TD><TD > add velocity info to buffer</TD></TR>
<TR><TD >pack_comm_one</TD><TD > store extra info unique to this atom style</TD></TR>
<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >unpack_comm_vel</TD><TD > also retrieve velocity info</TD></TR>
<TR><TD >unpack_comm_one</TD><TD > retreive extra info unique to this atom style</TD></TR>
<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces</TD></TR>
<TR><TD >pack_reverse_one</TD><TD > store extra info unique to this atom style</TD></TR>
<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >unpack_reverse_one</TD><TD > retreive extra info unique to this atom style</TD></TR>
<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds</TD></TR>
<TR><TD >pack_border_vel</TD><TD > add velocity info to buffer</TD></TR>
<TR><TD >pack_border_one</TD><TD > store extra info unique to this atom style</TD></TR>
<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >unpack_border_vel</TD><TD > also retrieve velocity info</TD></TR>
<TR><TD >unpack_border_one</TD><TD > retreive extra info unique to this atom style</TD></TR>
<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms</TD></TR>
<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer</TD></TR>
<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer</TD></TR>
<TR><TD >create_atom</TD><TD > create an individual atom of this style</TD></TR>
<TR><TD >data_atom</TD><TD > parse an atom line from the data file</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays
<TR><TD >init</TD><TD > one time setup (optional)</TD></TR>
<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths (required)</TD></TR>
<TR><TD >grow_reset</TD><TD > make array pointers in Atom and AtomVec classes consistent (required)</TD></TR>
<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations (required)</TD></TR>
<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep (required)</TD></TR>
<TR><TD >pack_comm_vel</TD><TD > add velocity info to communication buffer (required)</TD></TR>
<TR><TD >pack_comm_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >unpack_comm_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
<TR><TD >unpack_comm_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces (required)</TD></TR>
<TR><TD >pack_reverse_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >unpack_reverse_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds (required)</TD></TR>
<TR><TD >pack_border_vel</TD><TD > add velocity info to buffer (required)</TD></TR>
<TR><TD >pack_border_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >unpack_border_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
<TR><TD >unpack_border_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor (required)</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms (required)</TD></TR>
<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer (required)</TD></TR>
<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer (required)</TD></TR>
<TR><TD >create_atom</TD><TD > create an individual atom of this style (required)</TD></TR>
<TR><TD >data_atom</TD><TD > parse an atom line from the data file (required)</TD></TR>
<TR><TD >data_atom_hybrid</TD><TD > parse additional atom info unique to this atom style (optional)</TD></TR>
<TR><TD >data_vel</TD><TD > parse one line of velocity information from data file (optional)</TD></TR>
<TR><TD >data_vel_hybrid</TD><TD > parse additional velocity data unique to this atom style (optional)</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays (required)
</TD></TR></TABLE></DIV>
<P>The constructor of the derived class sets values for several variables
@ -192,7 +195,7 @@ modify.
</P>
<HR>
<A NAME = "bond"></A><H4>Bond, angle, dihedral, improper potentials
<A NAME = "mod_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
@ -202,21 +205,26 @@ add new potentials to LAMMPS.
the harmonic forms of the angle, dihedral, and improper style
commands.
</P>
<P>Here is a brief description of methods you define in your new derived
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
details.
<P>Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute</TD><TD > compute the molecular interactions</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one bond type</TD></TR>
<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE</TD></TR>
<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files</TD></TR>
<TR><TD >single</TD><TD > force and energy of a single bond
<TR><TD >init</TD><TD > check if all coefficients are set, calls <I>init_style</I> (optional)</TD></TR>
<TR><TD >init_style</TD><TD > check if style specific conditions are met (optional)</TD></TR>
<TR><TD >compute</TD><TD > compute the molecular interactions (required)</TD></TR>
<TR><TD >settings</TD><TD > apply global settings for all types (optional)</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one type (required)</TD></TR>
<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE (required, bond only)</TD></TR>
<TR><TD >equilibrium_angle</TD><TD > opening of angle, used by SHAKE (required, angle only)</TD></TR>
<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files (required)</TD></TR>
<TR><TD >single</TD><TD > force and energy of a single bond or angle (required, bond or angle only)</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory allocated by the style (optional)
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "compute"></A><H4>Compute styles
<A NAME = "mod_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
@ -232,21 +240,28 @@ per-atom kinetic energy.
class. See compute.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute_scalar</TD><TD > compute a scalar quantity</TD></TR>
<TR><TD >compute_vector</TD><TD > compute a vector of quantities</TD></TR>
<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack the buffer</TD></TR>
<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate</TD></TR>
<TR><TD >unpack_reverse</TD><TD > unpack the buffer</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory usage
<TR><TD >init</TD><TD > perform one time setup (required)</TD></TR>
<TR><TD >init_list</TD><TD > neighbor list setup, if needed (optional)</TD></TR>
<TR><TD >compute_scalar</TD><TD > compute a scalar quantity (optional)</TD></TR>
<TR><TD >compute_vector</TD><TD > compute a vector of quantities (optional)</TD></TR>
<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom (optional)</TD></TR>
<TR><TD >compute_local</TD><TD > compute one or more quantities per processor (optional)</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate (optional)</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack the buffer (optional)</TD></TR>
<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate (optional)</TD></TR>
<TR><TD >unpack_reverse</TD><TD > unpack the buffer (optional)</TD></TR>
<TR><TD >remove_bias</TD><TD > remove velocity bias from one atom (optional)</TD></TR>
<TR><TD >remove_bias_all</TD><TD > remove velocity bias from all atoms in group (optional)</TD></TR>
<TR><TD >restore_bias</TD><TD > restore velocity bias for one atom after remove_bias (optional)</TD></TR>
<TR><TD >restore_bias_all</TD><TD > same as before, but for all atoms in group (optional)</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory usage (optional)
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "dump"></A><H4>Dump styles
<A NAME = "mod_4"></A><H4>10.4 Dump styles
</H4>
<A NAME = "dump_custom"></A><H4>Dump custom output options
<A NAME = "mod_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 +292,7 @@ half-dozen or so locations where code will need to be added.
</P>
<HR>
<A NAME = "fix"></A><H4>Fix styles
<A NAME = "mod_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
@ -297,34 +312,59 @@ implement.
derived class. See fix.h for details.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep</TD></TR>
<TR><TD >init</TD><TD > initialization before a run</TD></TR>
<TR><TD >setup</TD><TD > called immediately before the 1st timestep</TD></TR>
<TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep</TD></TR>
<TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps</TD></TR>
<TR><TD >pre_neighbor</TD><TD > called before neighbor list build</TD></TR>
<TR><TD >post_force</TD><TD > called after pair & molecular forces are computed</TD></TR>
<TR><TD >final_integrate</TD><TD > called at end of each timestep</TD></TR>
<TR><TD >end_of_step</TD><TD > called at very end of timestep</TD></TR>
<TR><TD >write_restart</TD><TD > dumps fix info to restart file</TD></TR>
<TR><TD >restart</TD><TD > uses info from restart file to re-initialize the fix</TD></TR>
<TR><TD >grow_arrays</TD><TD > allocate memory for atom-based arrays used by fix</TD></TR>
<TR><TD >copy_arrays</TD><TD > copy atom info when an atom migrates to a new processor</TD></TR>
<TR><TD >memory_usage</TD><TD > report memory used by fix</TD></TR>
<TR><TD >pack_exchange</TD><TD > store atom's data in a buffer</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve atom's data from a buffer</TD></TR>
<TR><TD >pack_restart</TD><TD > store atom's data for writing to restart file</TD></TR>
<TR><TD >unpack_restart</TD><TD > retrieve atom's data from a restart file buffer</TD></TR>
<TR><TD >size_restart</TD><TD > size of atom's data</TD></TR>
<TR><TD >maxsize_restart</TD><TD > max size of atom's data</TD></TR>
<TR><TD >initial_integrate_respa</TD><TD > same as initial_integrate, but for rRESPA</TD></TR>
<TR><TD >post_force_respa</TD><TD > same as post_force, but for rRESPA</TD></TR>
<TR><TD >final_integrate_respa</TD><TD > same as final_integrate, but for rRESPA</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer to communicate a per-atom quantity</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity</TD></TR>
<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity</TD></TR>
<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity</TD></TR>
<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output
<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep (required)</TD></TR>
<TR><TD >init</TD><TD > initialization before a run (optional)</TD></TR>
<TR><TD >setup_pre_exchange</TD><TD > called before atom exchange in setup (optional)</TD></TR>
<TR><TD >setup_pre_force</TD><TD > called before force computation in setup (optional)</TD></TR>
<TR><TD >setup</TD><TD > called immediately before the 1st timestep and after forces are computed (optional)</TD></TR>
<TR><TD >min_setup_pre_force</TD><TD > like setup_pre_force, but for minimizations instead of MD runs (optional)</TD></TR>
<TR><TD >min_setup</TD><TD > like setup, but for minimizations instead of MD runs (optional)</TD></TR>
<TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep (optional)</TD></TR>
<TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps (optional)</TD></TR>
<TR><TD >pre_neighbor</TD><TD > called before neighbor list build (optional)</TD></TR>
<TR><TD >pre_force</TD><TD > called after pair & molecular forces are computed (optional)</TD></TR>
<TR><TD >post_force</TD><TD > called after pair & molecular forces are computed and communicated (optional)</TD></TR>
<TR><TD >final_integrate</TD><TD > called at end of each timestep (optional)</TD></TR>
<TR><TD >end_of_step</TD><TD > called at very end of timestep (optional)</TD></TR>
<TR><TD >write_restart</TD><TD > dumps fix info to restart file (optional)</TD></TR>
<TR><TD >restart</TD><TD > uses info from restart file to re-initialize the fix (optional)</TD></TR>
<TR><TD >grow_arrays</TD><TD > allocate memory for atom-based arrays used by fix (optional)</TD></TR>
<TR><TD >copy_arrays</TD><TD > copy atom info when an atom migrates to a new processor (optional)</TD></TR>
<TR><TD >pack_exchange</TD><TD > store atom's data in a buffer (optional)</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve atom's data from a buffer (optional)</TD></TR>
<TR><TD >pack_restart</TD><TD > store atom's data for writing to restart file (optional)</TD></TR>
<TR><TD >unpack_restart</TD><TD > retrieve atom's data from a restart file buffer (optional)</TD></TR>
<TR><TD >size_restart</TD><TD > size of atom's data (optional)</TD></TR>
<TR><TD >maxsize_restart</TD><TD > max size of atom's data (optional)</TD></TR>
<TR><TD >setup_pre_force_respa</TD><TD > same as setup_pre_force, but for rRESPA (optional)</TD></TR>
<TR><TD >initial_integrate_respa</TD><TD > same as initial_integrate, but for rRESPA (optional)</TD></TR>
<TR><TD >post_integrate_respa</TD><TD > called after the first half integration step is done in rRESPA (optional)</TD></TR>
<TR><TD >pre_force_respa</TD><TD > same as pre_force, but for rRESPA (optional)</TD></TR>
<TR><TD >post_force_respa</TD><TD > same as post_force, but for rRESPA (optional)</TD></TR>
<TR><TD >final_integrate_respa</TD><TD > same as final_integrate, but for rRESPA (optional)</TD></TR>
<TR><TD >min_pre_force</TD><TD > called after pair & molecular forces are computed in minimizer (optional)</TD></TR>
<TR><TD >min_post_force</TD><TD > called after pair & molecular forces are computed and communicated in minmizer (optional)</TD></TR>
<TR><TD >min_store</TD><TD > store extra data for linesearch based minimization on a LIFO stack (optional)</TD></TR>
<TR><TD >min_pushstore</TD><TD > push the minimization LIFO stack one element down (optional)</TD></TR>
<TR><TD >min_popstore</TD><TD > pop the minimization LIFO stack one element up (optional)</TD></TR>
<TR><TD >min_clearstore</TD><TD > clear minimization LIFO stack (optional)</TD></TR>
<TR><TD >min_step</TD><TD > reset or move forward on line search minimization (optional)</TD></TR>
<TR><TD >min_dof</TD><TD > report number of degrees of freedom <I>added</I> by this fix in minimization (optional)</TD></TR>
<TR><TD >max_alpha</TD><TD > report maximum allowed step size during linesearch minimization (optional)</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer to communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
<TR><TD >dof</TD><TD > report number of degrees of freedom <I>removed</I> by this fix during MD (optional)</TD></TR>
<TR><TD >compute_scalar</TD><TD > return a global scalar property that the fix computes (optional)</TD></TR>
<TR><TD >compute_vector</TD><TD > return a component of a vector property that the fix computes (optional)</TD></TR>
<TR><TD >compute_array</TD><TD > return a component of an array property that the fix computes (optional)</TD></TR>
<TR><TD >deform</TD><TD > called when the box size is changed (optional)</TD></TR>
<TR><TD >reset_target</TD><TD > called when a change of the target temperature is requested during a run (optional)</TD></TR>
<TR><TD >reset_dt</TD><TD > is called when a change of the time step is requested during a run (optional)</TD></TR>
<TR><TD >modify_param</TD><TD > called when a fix_modify request is executed (optional)</TD></TR>
<TR><TD >memory_usage</TD><TD > report memory used by fix (optional)</TD></TR>
<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output (optional)
</TD></TR></TABLE></DIV>
<P>Typically, only a small fraction of these methods are defined for a
@ -355,7 +395,7 @@ 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 = "mod_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 +417,7 @@ needed.
</P>
<HR>
<A NAME = "kspace"></A><H4>Kspace computations
<A NAME = "mod_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 +437,7 @@ class. See kspace.h for details.
<HR>
<A NAME = "min"></A><H4>Minimization solvers
<A NAME = "mod_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 +456,7 @@ class. See min.h for details.
<HR>
<A NAME = "pair"></A><H4>Pairwise potentials
<A NAME = "mod_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 +485,7 @@ includes some optional methods to enable its use with rRESPA.
</P>
<HR>
<A NAME = "region"></A><H4>Region styles
<A NAME = "mod_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 +503,7 @@ class. See region.h for details.
<HR>
<A NAME = "thermo"></A><H4>Thermodynamic output options
<A NAME = "mod_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 +532,7 @@ by adding a new keyword to the thermo command.
</P>
<HR>
<A NAME = "variable"></A><H4>Variable options
<A NAME = "mod_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
@ -532,19 +572,21 @@ 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 = "mod_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
you think the features will be of interest to other users. If they
are broadly useful we may add them as core files to LAMMPS or as part
of a <A HREF = "Section_start.html#2_3">standard package</A>. Else we will add them
as a user-contributed package or file. Examples of user packages are
in src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
simplest way to have your contribution quickly added to the LAMMPS
distribution. You can see a list of the both standard and user
packages by typing "make package" in the LAMMPS src directory.
of a <A HREF = "Section_start.html#start_3">standard package</A>. Else we will add
them as a user-contributed package or file. Examples of user packages
are in src sub-directories that start with USER. The USER-MISC
package is simply a collection of (mostly) unrelated single files,
which is the simplest way to have your contribution quickly added to
the LAMMPS distribution. You can see a list of the both standard and
user packages by typing "make package" in the LAMMPS src directory.
</P>
<P>With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source

301
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
@ -19,7 +19,7 @@ with minimal instructions. If you add a new feature to LAMMPS and
think it will be of interest to general users, we encourage you to
submit it to the developers for inclusion in the released version of
LAMMPS. Information about how to do this is provided
"below"_#package.
"below"_#mod_14.
The best way to add a new feature is to find a similar feature in
LAMMPS and look at the corresponding source and header files to figure
@ -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
@ -135,50 +110,78 @@ 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"_#mod_1
10.2 "Bond, angle, dihedral, improper potentials"_#mod_2
10.3 "Compute styles"_#mod_3
10.4 "Dump styles"_#mod_4
10.5 "Dump custom output options"_#mod_5
10.6 "Fix styles"_#mod_6 which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
10.7 "Input script commands"_mod_7
10.8 "Kspace computations"_#mod_8
10.9 "Minimization styles"_#mod_9
10.10 "Pairwise potentials"_#mod_10
10.11 "Region styles"_#mod_11
10.12 "Thermodynamic output options"_#mod_12
10.13 "Variable options"_#mod_13
10.14 "Submitting new features for inclusion in LAMMPS"_#mod_14 :all(b)
:line
:line
Atom styles :link(atom),h4
10.1 Atom styles :link(mod_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.
A new atom style can be created if one of the existing atom styles
does not define all the arrays you need to store and communicate with
atoms.
Classes that define an atom style are derived from the AtomVec class
and managed by the Atom class. The atom style determines what
quantities are associated with an atom. A new atom style can be
created if one of the existing atom styles does not define all
the arrays you need to store and communicate with atoms.
Atom_vec_atomic.cpp is a simple example of an atom style.
Here is a brief description of methods you define in your new derived
class. See atom.h for details.
class. See atom_vec.h for details.
grow: re-allocate atom arrays to longer lengths
copy: copy info for one atom to another atom's array locations
pack_comm: store an atom's info in a buffer communicated every timestep
pack_comm_vel: add velocity info to buffer
pack_comm_one: store extra info unique to this atom style
unpack_comm: retrieve an atom's info from the buffer
unpack_comm_vel: also retrieve velocity info
unpack_comm_one: retreive extra info unique to this atom style
pack_reverse: store an atom's info in a buffer communicating partial forces
pack_reverse_one: store extra info unique to this atom style
unpack_reverse: retrieve an atom's info from the buffer
unpack_reverse_one: retreive extra info unique to this atom style
pack_border: store an atom's info in a buffer communicated on neighbor re-builds
pack_border_vel: add velocity info to buffer
pack_border_one: store extra info unique to this atom style
unpack_border: retrieve an atom's info from the buffer
unpack_border_vel: also retrieve velocity info
unpack_border_one: retreive extra info unique to this atom style
pack_exchange: store all an atom's info to migrate to another processor
unpack_exchange: retrieve an atom's info from the buffer
size_restart: number of restart quantities associated with proc's atoms
pack_restart: pack atom quantities into a buffer
unpack_restart: unpack atom quantities from a buffer
create_atom: create an individual atom of this style
data_atom: parse an atom line from the data file
memory_usage: tally memory allocated by atom arrays :tb(s=:)
init: one time setup (optional)
grow: re-allocate atom arrays to longer lengths (required)
grow_reset: make array pointers in Atom and AtomVec classes consistent (required)
copy: copy info for one atom to another atom's array locations (required)
pack_comm: store an atom's info in a buffer communicated every timestep (required)
pack_comm_vel: add velocity info to communication buffer (required)
pack_comm_hybrid: store extra info unique to this atom style (optional)
unpack_comm: retrieve an atom's info from the buffer (required)
unpack_comm_vel: also retrieve velocity info (required)
unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
pack_reverse: store an atom's info in a buffer communicating partial forces (required)
pack_reverse_hybrid: store extra info unique to this atom style (optional)
unpack_reverse: retrieve an atom's info from the buffer (required)
unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
pack_border_vel: add velocity info to buffer (required)
pack_border_hybrid: store extra info unique to this atom style (optional)
unpack_border: retrieve an atom's info from the buffer (required)
unpack_border_vel: also retrieve velocity info (required)
unpack_border_hybrid: retreive extra info unique to this atom style (optional)
pack_exchange: store all an atom's info to migrate to another processor (required)
unpack_exchange: retrieve an atom's info from the buffer (required)
size_restart: number of restart quantities associated with proc's atoms (required)
pack_restart: pack atom quantities into a buffer (required)
unpack_restart: unpack atom quantities from a buffer (required)
create_atom: create an individual atom of this style (required)
data_atom: parse an atom line from the data file (required)
data_atom_hybrid: parse additional atom info unique to this atom style (optional)
data_vel: parse one line of velocity information from data file (optional)
data_vel_hybrid: parse additional velocity data unique to this atom style (optional)
memory_usage: tally memory allocated by atom arrays (required) :tb(s=:)
The constructor of the derived class sets values for several variables
that you must set when defining a new atom style, which are documented
@ -188,7 +191,7 @@ modify.
:line
Bond, angle, dihedral, improper potentials :link(bond),h4
10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4
Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
@ -198,19 +201,24 @@ Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
Here is a brief description of methods you define in your new derived
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
details.
Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
compute: compute the molecular interactions
coeff: set coefficients for one bond type
equilibrium_distance: length of bond, used by SHAKE
write & read_restart: writes/reads coeffs to restart files
single: force and energy of a single bond :tb(s=:)
init: check if all coefficients are set, calls {init_style} (optional)
init_style: check if style specific conditions are met (optional)
compute: compute the molecular interactions (required)
settings: apply global settings for all types (optional)
coeff: set coefficients for one type (required)
equilibrium_distance: length of bond, used by SHAKE (required, bond only)
equilibrium_angle: opening of angle, used by SHAKE (required, angle only)
write & read_restart: writes/reads coeffs to restart files (required)
single: force and energy of a single bond or angle (required, bond or angle only)
memory_usage: tally memory allocated by the style (optional) :tb(s=:)
:line
Compute styles :link(compute),h4
10.3 Compute styles :link(mod_3),h4
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
@ -225,19 +233,26 @@ per-atom kinetic energy.
Here is a brief description of methods you define in your new derived
class. See compute.h for details.
compute_scalar: compute a scalar quantity
compute_vector: compute a vector of quantities
compute_peratom: compute one or more quantities per atom
pack_comm: pack a buffer with items to communicate
unpack_comm: unpack the buffer
pack_reverse: pack a buffer with items to reverse communicate
unpack_reverse: unpack the buffer
memory_usage: tally memory usage :tb(s=:)
init: perform one time setup (required)
init_list: neighbor list setup, if needed (optional)
compute_scalar: compute a scalar quantity (optional)
compute_vector: compute a vector of quantities (optional)
compute_peratom: compute one or more quantities per atom (optional)
compute_local: compute one or more quantities per processor (optional)
pack_comm: pack a buffer with items to communicate (optional)
unpack_comm: unpack the buffer (optional)
pack_reverse: pack a buffer with items to reverse communicate (optional)
unpack_reverse: unpack the buffer (optional)
remove_bias: remove velocity bias from one atom (optional)
remove_bias_all: remove velocity bias from all atoms in group (optional)
restore_bias: restore velocity bias for one atom after remove_bias (optional)
restore_bias_all: same as before, but for all atoms in group (optional)
memory_usage: tally memory usage (optional) :tb(s=:)
:line
Dump styles :link(dump),h4
Dump custom output options :link(dump_custom),h4
10.4 Dump styles :link(mod_4),h4
10.5 Dump custom output options :link(mod_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 +281,7 @@ half-dozen or so locations where code will need to be added.
:line
Fix styles :link(fix),h4
10.6 Fix styles :link(mod_6),h4
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
@ -285,34 +300,59 @@ implement.
Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
setmask: determines when the fix is called during the timestep
init: initialization before a run
setup: called immediately before the 1st timestep
initial_integrate: called at very beginning of each timestep
pre_exchange: called before atom exchange on re-neighboring steps
pre_neighbor: called before neighbor list build
post_force: called after pair & molecular forces are computed
final_integrate: called at end of each timestep
end_of_step: called at very end of timestep
write_restart: dumps fix info to restart file
restart: uses info from restart file to re-initialize the fix
grow_arrays: allocate memory for atom-based arrays used by fix
copy_arrays: copy atom info when an atom migrates to a new processor
memory_usage: report memory used by fix
pack_exchange: store atom's data in a buffer
unpack_exchange: retrieve atom's data from a buffer
pack_restart: store atom's data for writing to restart file
unpack_restart: retrieve atom's data from a restart file buffer
size_restart: size of atom's data
maxsize_restart: max size of atom's data
initial_integrate_respa: same as initial_integrate, but for rRESPA
post_force_respa: same as post_force, but for rRESPA
final_integrate_respa: same as final_integrate, but for rRESPA
pack_comm: pack a buffer to communicate a per-atom quantity
unpack_comm: unpack a buffer to communicate a per-atom quantity
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity
thermo: compute quantities for thermodynamic output :tb(s=:)
setmask: determines when the fix is called during the timestep (required)
init: initialization before a run (optional)
setup_pre_exchange: called before atom exchange in setup (optional)
setup_pre_force: called before force computation in setup (optional)
setup: called immediately before the 1st timestep and after forces are computed (optional)
min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional)
min_setup: like setup, but for minimizations instead of MD runs (optional)
initial_integrate: called at very beginning of each timestep (optional)
pre_exchange: called before atom exchange on re-neighboring steps (optional)
pre_neighbor: called before neighbor list build (optional)
pre_force: called after pair & molecular forces are computed (optional)
post_force: called after pair & molecular forces are computed and communicated (optional)
final_integrate: called at end of each timestep (optional)
end_of_step: called at very end of timestep (optional)
write_restart: dumps fix info to restart file (optional)
restart: uses info from restart file to re-initialize the fix (optional)
grow_arrays: allocate memory for atom-based arrays used by fix (optional)
copy_arrays: copy atom info when an atom migrates to a new processor (optional)
pack_exchange: store atom's data in a buffer (optional)
unpack_exchange: retrieve atom's data from a buffer (optional)
pack_restart: store atom's data for writing to restart file (optional)
unpack_restart: retrieve atom's data from a restart file buffer (optional)
size_restart: size of atom's data (optional)
maxsize_restart: max size of atom's data (optional)
setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional)
initial_integrate_respa: same as initial_integrate, but for rRESPA (optional)
post_integrate_respa: called after the first half integration step is done in rRESPA (optional)
pre_force_respa: same as pre_force, but for rRESPA (optional)
post_force_respa: same as post_force, but for rRESPA (optional)
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore: push the minimization LIFO stack one element down (optional)
min_popstore: pop the minimization LIFO stack one element up (optional)
min_clearstore: clear minimization LIFO stack (optional)
min_step: reset or move forward on line search minimization (optional)
min_dof: report number of degrees of freedom {added} by this fix in minimization (optional)
max_alpha: report maximum allowed step size during linesearch minimization (optional)
pack_comm: pack a buffer to communicate a per-atom quantity (optional)
unpack_comm: unpack a buffer to communicate a per-atom quantity (optional)
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional)
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional)
dof: report number of degrees of freedom {removed} by this fix during MD (optional)
compute_scalar: return a global scalar property that the fix computes (optional)
compute_vector: return a component of a vector property that the fix computes (optional)
compute_array: return a component of an array property that the fix computes (optional)
deform: called when the box size is changed (optional)
reset_target: called when a change of the target temperature is requested during a run (optional)
reset_dt: is called when a change of the time step is requested during a run (optional)
modify_param: called when a fix_modify request is executed (optional)
memory_usage: report memory used by fix (optional)
thermo: compute quantities for thermodynamic output (optional) :tb(s=:)
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
@ -342,7 +382,7 @@ 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(mod_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 +402,7 @@ needed.
:line
Kspace computations :link(kspace),h4
10.8 Kspace computations :link(mod_8),h4
Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
@ -380,7 +420,7 @@ memory_usage: tally of memory usage :tb(s=:)
:line
Minimization solvers :link(min),h4
10.9 Minimization styles :link(mod_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 +437,7 @@ memory_usage: tally of memory usage :tb(s=:)
:line
Pairwise potentials :link(pair),h4
10.10 Pairwise potentials :link(mod_10),h4
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
@ -424,7 +464,7 @@ The inner/middle/outer routines are optional.
:line
Region styles :link(region),h4
10.11 Region styles :link(mod_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 +480,7 @@ match: determine whether a point is in the region :tb(s=:)
:line
Thermodynamic output options :link(thermo),h4
10.12 Thermodynamic output options :link(mod_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 +509,7 @@ by adding a new keyword to the thermo command.
:line
Variable options :link(variable),h4
10.13 Variable options :link(mod_13),h4
There is one class that computes and stores "variable"_variable.html
information in LAMMPS; see the file variable.cpp. The value
@ -507,21 +547,22 @@ 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(mod_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
you think the features will be of interest to other users. If they
are broadly useful we may add them as core files to LAMMPS or as part
of a "standard package"_Section_start.html#2_3. Else we will add them
as a user-contributed package or file. Examples of user packages are
in src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
simplest way to have your contribution quickly added to the LAMMPS
distribution. You can see a list of the both standard and user
packages by typing "make package" in the LAMMPS src directory.
of a "standard package"_Section_start.html#start_3. Else we will add
them as a user-contributed package or file. Examples of user packages
are in src sub-directories that start with USER. The USER-MISC
package is simply a collection of (mostly) unrelated single files,
which is the simplest way to have your contribution quickly added to
the LAMMPS distribution. You can see a list of the both standard and
user packages by typing "make package" in the LAMMPS src directory.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source

404
doc/Section_packages.html Normal file
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@ -0,0 +1,404 @@
<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_accelerate.html">Next
Section</A>
</CENTER>
<HR>
<H3>4. Packages
</H3>
<P>LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
</P>
<P>See <A HREF = "Section_start.html#start_3">this section</A> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages in LAMMPS.
</P>
<P>Below, the packages currently availabe in LAMMPS are listed. For
standard packages, just a one-line description is given. For user
packages, more details are provided.
</P>
4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
4.2 <A HREF = "#pkg_2">User packages</A> <BR>
<HR>
<HR>
<H4><A NAME = "pkg_1"></A>4.1 Standard packages
</H4>
<P>The current list of standard packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">howto</A></TD><TD > ellipse</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">howto</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (1)</TD><TD > <A HREF = "Section_accelerate.html#acc_1">howto</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">howto</A></TD><TD > tad</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(1) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package.
</P>
<P>The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
</P>
<P>The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This section</A> of the manual gives details on the 2-step build process with external libraries.
</P>
<HR>
<HR>
<H4><A NAME = "pkg_2"></A>4.2 User packages
</H4>
<P>The current list of user-contributed packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_cmm.html">pair_style cg/cmm</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EWALDN</TD><TD > Ewald for 1/R^n</TD><TD > Pieter in' t Veld (BASF)</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_2">accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">SPH_LAMMPS_userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided witht he package.
</P>
<P>The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.
</P>
<P>The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. These are in the
lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This
section</A> of the manual gives details on
the 2-step build process with external libraries.
</P>
<P>More details on each package, from the USER-blah/README file
is given below.
</P>
<HR>
<H4>USER-MISC package
</H4>
<P>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (*.cpp and *.h).
</P>
<P>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
</P>
<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
</P>
<P>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
</P>
<P>The list of features and author of each is given in the
src/USER-MISC/README file.
</P>
<P>You should contact the author directly if you have specific questions
about the feature or its coding.
</P>
<HR>
<H4>USER-ATC package
</H4>
<P>This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.
</P>
<P>See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.
</P>
<P>There are example scripts for using this package in examples/USER/atc.
</P>
<P>This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
</P>
<HR>
<H4>USER-AWPMD package
</H4>
<P>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
</P>
<P>See the doc page for the pair_style awpmd/cut command to get started.
</P>
<P>There are example scripts for using this package in examples/USER/awpmd.
</P>
<P>This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-CG-CMM package
</H4>
<P>This package implements 4 commands which can be used in a LAMMPS input
script:
</P>
<UL><LI>pair_style cg/cmm
<LI>pair_style cg/cmm/coul/cut
<LI>pair_style cg/cmm/coul/long
<LI>angle_style cg/cmm
</UL>
<P>These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids (to be published soon).
</P>
<P>See the doc pages for these commands for details.
</P>
<P>There are example scripts for using this package in
examples/USER/cg-cmm.
</P>
<P>The current version of this package should be considered beta
quality. The CG potentials work correctly and well, but there will be
optimizations, cleanups and additional tools to aid in setting up and
analyzing simulations with this package added in the next months.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-CUDA package
</H4>
<P>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_4">Section_accelerate</A>
</P>
<P>There are example scripts for using this package in
examples/USER/cuda.
</P>
<P>This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-EFF package
</H4>
<P>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.
</P>
<P>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
</P>
<P>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
</P>
<P>See the doc page for the pair_style eff/cut command to get started.
</P>
<P>There are example scripts for using this package in
examples/USER/eff.
</P>
<P>There are auxiliary tools for using this package in tools/eff.
</P>
<P>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-EWALDN package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
</P>
<P>The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
</P>
<P>Another advantage of kspace_style ewald/n is that it can be used with
non-orthogonal (triclinic symmetry) simulation boxes, either for just
long-range Coulombic interactions, or for both Coulombic and 1/r^N LJ
or Buckingham, which is not currently possible for other kspace styles
such as PPPM and ewald.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
</P>
<HR>
<H4>USER-OMP package
</H4>
<P>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_2">Section_accelerate</A>
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-REAXC package
</H4>
<P>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
</P>
<P>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
</P>
<P>The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
</P>
<P>For technical details about this implemention of ReaxFF, see
this paper:
</P>
<P>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
</P>
<P>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
</P>
<P>The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
</P>
<HR>
<H4>USER-SPH package
</H4>
<P>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
</P>
<P>* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
* plain or Monaghans XSPH integration of the equations of motion
* density continuity or density summation to propagate the density field
* commands to set internal energy and density of particles from the
input script
* output commands to access internal energy and density for dumping and
thermo output
</P>
<P>See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/sph.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
</HTML>

390
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@ -0,0 +1,390 @@
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_accelerate.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
4. Packages :h3
LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
See "this section"_Section_start.html#start_3 of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages in LAMMPS.
Below, the packages currently availabe in LAMMPS are listed. For
standard packages, just a one-line description is given. For user
packages, more details are provided.
4.1 "Standard packages"_#pkg_1
4.2 "User packages"_#pkg_2 :all(b)
:line
:line
4.1 Standard packages :h4,link(pkg_1)
The current list of standard packages is as follows:
Package, Description, Author(s), Doc page, Example, Library
ASPHERE, aspherical particles, -, "howto"_Section_howto.html#howto_14, ellipse, -
CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
GPU, GPU-enabled potentials, Mike Brown (ORNL), "accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu
GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, -
KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
MOLECULE, molecular system force fields, -, "howto"_Section_howto.html#howto_3, peptide, -
OPT, optimized pair potentials, Fischer & Richie & Natoli (1), "howto"_Section_accelerate.html#acc_1, -, -
PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
REPLICA, multi-replica methods, -, "howto"_Section_howto.html#howto_5, tad, -
SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
XTC, dumps in XTC format, -, "dump"_dump.html, -, -
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
(1) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
command implemented as part of the package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. "This section"_Section_start.html#start_3_3 of the manual gives details on the 2-step build process with external libraries.
:line
:line
4.2 User packages :h4,link(pkg_2)
The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
USER-MISC, single-file contributions, USER-MISC/README, -, -, -, -
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style cg/cmm"_pair_cmm.html, USER/cg-cmm, "cg"_cg, -
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "accelerate"_Section_accelerate.html#acc_4, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-EWALDN, Ewald for 1/R^n, Pieter in' t Veld (BASF), "kspace_style"_kspace_style.html, -, -, -
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "accelerate"_Section_accelerate.html#acc_2, -, -, -
USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH_LAMMPS_userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
:tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc)
:link(cg,http://lammps.sandia.gov/pictures.html#cg)
:link(eff,http://lammps.sandia.gov/movies.html#eff)
:link(sph,http://lammps.sandia.gov/movies.html#sph)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided witht he package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. These are in the
lib directory of the distribution. "This
section"_Section_start.html#start_3_3 of the manual gives details on
the 2-step build process with external libraries.
More details on each package, from the USER-blah/README file
is given below.
:line
USER-MISC package :h4
The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (*.cpp and *.h).
More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
"Section_commands"_Section_commands.html#cmd_5
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
The list of features and author of each is given in the
src/USER-MISC/README file.
You should contact the author directly if you have specific questions
about the feature or its coding.
:line
USER-ATC package :h4
This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.
See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.
There are example scripts for using this package in examples/USER/atc.
This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
:line
USER-AWPMD package :h4
This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
See the doc page for the pair_style awpmd/cut command to get started.
There are example scripts for using this package in examples/USER/awpmd.
This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
:line
USER-CG-CMM package :h4
This package implements 4 commands which can be used in a LAMMPS input
script:
pair_style cg/cmm
pair_style cg/cmm/coul/cut
pair_style cg/cmm/coul/long
angle_style cg/cmm :ul
These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids (to be published soon).
See the doc pages for these commands for details.
There are example scripts for using this package in
examples/USER/cg-cmm.
The current version of this package should be considered beta
quality. The CG potentials work correctly and well, but there will be
optimizations, cleanups and additional tools to aid in setting up and
analyzing simulations with this package added in the next months.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-CUDA package :h4
This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_4
There are example scripts for using this package in
examples/USER/cuda.
This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.
:line
USER-EFF package :h4
This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
See the doc page for the pair_style eff/cut command to get started.
There are example scripts for using this package in
examples/USER/eff.
There are auxiliary tools for using this package in tools/eff.
The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
:line
USER-EWALDN package :h4
This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
Another advantage of kspace_style ewald/n is that it can be used with
non-orthogonal (triclinic symmetry) simulation boxes, either for just
long-range Coulombic interactions, or for both Coulombic and 1/r^N LJ
or Buckingham, which is not currently possible for other kspace styles
such as PPPM and ewald.
See the doc pages for these commands for details.
The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
:line
USER-OMP package :h4
This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_2
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-REAXC package :h4
This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
:line
USER-SPH package :h4
This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
* plain or Monaghans XSPH integration of the equations of motion
* density continuity or density summation to propagate the density field
* commands to set internal energy and density of particles from the
input script
* output commands to access internal energy and density for dumping and
thermo output
See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
There are example scripts for using this package in examples/USER/sph.
The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.

2
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@ -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
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@ -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

55
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@ -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
@ -20,16 +20,17 @@ either from a Python script or interactively from a Python prompt.
<P><A HREF = "http://www.python.org">Python</A> is a powerful scripting and programming
language which can be used to wrap software like LAMMPS and other
packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#4_10">this
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#howto_10">this
section</A> of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See <A HREF = "Section_start.html#2_4">this section</A> about how to
build LAMMPS as a library, and <A HREF = "Section_howto.html#4_19">this section</A>
for a description of the library interface provided in src/library.cpp
and src/library.h and how to extend it for your needs. As described
below, that interface is what is exposed to Python. It is designed to
be easy to add functions to. This has the effect of extending the
Python inteface as well. See details below.
other codes. See <A HREF = "Section_start.html#start_4">this section</A> about how
to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
section</A> for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
is exposed to Python. It is designed to be easy to add functions to.
This has the effect of extending the Python inteface as well. See
details below.
</P>
<P>By using the Python interface LAMMPS can also be coupled with a GUI or
visualization tools that display graphs or animations in real time as
@ -88,13 +89,13 @@ 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 = "#py_1">Extending Python with a serial version of LAMMPS</A>
<LI>11.2 <A HREF = "#py_2">Creating a shared MPI library</A>
<LI>11.3 <A HREF = "#py_3">Extending Python with a parallel version of LAMMPS</A>
<LI>11.4 <A HREF = "#py_4">Extending Python with MPI</A>
<LI>11.5 <A HREF = "#py_5">Testing the Python-LAMMPS interface</A>
<LI>11.6 <A HREF = "#py_6">Using LAMMPS from Python</A>
<LI>11.7 <A HREF = "#py_7">Example Python scripts that use LAMMPS</A>
</UL>
<P>Before proceeding, there are 2 items to note.
</P>
@ -116,7 +117,7 @@ code, you are not building shared versions of these libraries.
</P>
<P>The discussion below describes how to create a shared MPI library. I
suggest you start by configuing LAMMPS without packages installed that
require any libraries besides MPI. See <A HREF = "Section_start.html#2_3">this
require any libraries besides MPI. See <A HREF = "Section_start.html#start_3">this
section</A> of the manual for a discussion of
LAMMPS pacakges. E.g. do not use the KSPACE, GPU, MEAM, POEMS, or
REAX packages.
@ -134,7 +135,7 @@ LAMMPS wrapper.
<HR>
<A NAME = "9_1"></A><H4>Extending Python with a serial version of LAMMPS
<A NAME = "py_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 +165,7 @@ 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 = "py_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 +196,7 @@ stand-alone code.
</P>
<HR>
<A NAME = "9_3"></A><H4>Extending Python with a parallel version of LAMMPS
<A NAME = "py_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
</H4>
<P>From the python directory, type
</P>
@ -233,7 +234,7 @@ will be put in the appropriate directory.
</P>
<HR>
<A NAME = "9_4"></A><H4>Extending Python with MPI
<A NAME = "py_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 +309,7 @@ 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 = "py_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 +403,7 @@ Python on a single processor, not in parallel.
<HR>
<A NAME = "9_6"></A><H4>Using LAMMPS from Python
<A NAME = "py_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
@ -498,7 +499,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See <A HREF = "Section_howto.html#4_15">this section</A> of the manual for a
See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
@ -578,7 +579,7 @@ following steps:
src/library.h.
<LI>Verify the new function is syntactically correct by building LAMMPS as
a library - see <A HREF = "Section_start.html#2_4">this section</A> of the
a library - see <A HREF = "Section_start.html#start_4">this section</A> of the
manual.
<LI>Add a wrapper method in the Python LAMMPS module to python/lammps.py
@ -594,7 +595,7 @@ Python script. Isn't ctypes amazing?
<HR>
<A NAME = "9_7"></A><H4>Example Python scripts that use LAMMPS
<A NAME = "py_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

55
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@ -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
@ -18,15 +18,16 @@ either from a Python script or interactively from a Python prompt.
language which can be used to wrap software like LAMMPS and other
packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See "this
section"_Section_howto.html#4_10 of the manual and the couple
section"_Section_howto.html#howto_10 of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See "this section"_Section_start.html#2_4 about how to
build LAMMPS as a library, and "this section"_Section_howto.html#4_19
for a description of the library interface provided in src/library.cpp
and src/library.h and how to extend it for your needs. As described
below, that interface is what is exposed to Python. It is designed to
be easy to add functions to. This has the effect of extending the
Python inteface as well. See details below.
other codes. See "this section"_Section_start.html#start_4 about how
to build LAMMPS as a library, and "this
section"_Section_howto.html#howto_19 for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
is exposed to Python. It is designed to be easy to add functions to.
This has the effect of extending the Python inteface as well. See
details below.
By using the Python interface LAMMPS can also be coupled with a GUI or
visualization tools that display graphs or animations in real time as
@ -85,13 +86,13 @@ 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"_#py_1
11.2 "Creating a shared MPI library"_#py_2
11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
11.4 "Extending Python with MPI"_#py_4
11.5 "Testing the Python-LAMMPS interface"_#py_5
11.6 "Using LAMMPS from Python"_#py_6
11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
Before proceeding, there are 2 items to note.
@ -114,7 +115,7 @@ code, you are not building shared versions of these libraries.
The discussion below describes how to create a shared MPI library. I
suggest you start by configuing LAMMPS without packages installed that
require any libraries besides MPI. See "this
section"_Section_start.html#2_3 of the manual for a discussion of
section"_Section_start.html#start_3 of the manual for a discussion of
LAMMPS pacakges. E.g. do not use the KSPACE, GPU, MEAM, POEMS, or
REAX packages.
@ -130,7 +131,7 @@ 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(py_1),h4
From the python directory in the LAMMPS distribution, type
@ -160,7 +161,7 @@ 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(py_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 +192,7 @@ 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(py_3),h4
From the python directory, type
@ -229,7 +230,7 @@ will be put in the appropriate directory.
:line
Extending Python with MPI :link(9_4),h4
11.4 Extending Python with MPI :link(py_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 +305,7 @@ 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(py_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 +398,7 @@ 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(py_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
@ -493,7 +494,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See "this section"_Section_howto.html#4_15 of the manual for a
See "this section"_Section_howto.html#howto_15 of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
"computes"_compute.html and "fixes"_fix.html for a description of what
@ -573,7 +574,7 @@ Add a new interface function to src/library.cpp and
src/library.h. :ulb,l
Verify the new function is syntactically correct by building LAMMPS as
a library - see "this section"_Section_start.html#2_4 of the
a library - see "this section"_Section_start.html#start_4 of the
manual. :l
Add a wrapper method in the Python LAMMPS module to python/lammps.py
@ -588,7 +589,7 @@ 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(py_7),h4
These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of

259
doc/Section_start.html
View File

@ -14,18 +14,18 @@
<P>This section describes how to build and run LAMMPS, for both new and
experienced users.
</P>
2.1 <A HREF = "#2_1">What's in the LAMMPS distribution</A><BR>
2.2 <A HREF = "#2_2">Making LAMMPS</A><BR>
2.3 <A HREF = "#2_3">Making LAMMPS with optional packages</A><BR>
2.4 <A HREF = "#2_4">Building LAMMPS as a library</A><BR>
2.5 <A HREF = "#2_5">Running LAMMPS</A><BR>
2.6 <A HREF = "#2_6">Command-line options</A><BR>
2.7 <A HREF = "#2_7">Screen output</A><BR>
2.8 <A HREF = "#2_8">Tips for users of previous versions</A> <BR>
2.1 <A HREF = "#start_1">What's in the LAMMPS distribution</A><BR>
2.2 <A HREF = "#start_2">Making LAMMPS</A><BR>
2.3 <A HREF = "#start_3">Making LAMMPS with optional packages</A><BR>
2.4 <A HREF = "#start_4">Building LAMMPS as a library</A><BR>
2.5 <A HREF = "#start_5">Running LAMMPS</A><BR>
2.6 <A HREF = "#start_6">Command-line options</A><BR>
2.7 <A HREF = "#start_7">Screen output</A><BR>
2.8 <A HREF = "#start_8">Tips for users of previous versions</A> <BR>
<HR>
<H4><A NAME = "2_1"></A>2.1 What's in the LAMMPS distribution
<H4><A NAME = "start_1"></A>2.1 What's in the LAMMPS distribution
</H4>
<P>When you download LAMMPS you will need to unzip and untar the
downloaded file with the following commands, after placing the file in
@ -54,8 +54,8 @@ then you just get a single file:
</P>
<PRE>lmp_windows.exe
</PRE>
<P>Skip to the <A HREF = "#2_5">Running LAMMPS</A> sections for info on how to launch
these executables on a Windows box.
<P>Skip to the <A HREF = "#start_5">Running LAMMPS</A> sections for info on how to
launch these executables on a Windows box.
</P>
<P>The Windows executables for serial or parallel only include certain
packages and bug-fixes/upgrades listed on <A HREF = "http://lammps.sandia.gov/bug.html">this
@ -67,20 +67,20 @@ as described in the next section.
</P>
<HR>
<H4><A NAME = "2_2"></A>2.2 Making LAMMPS
<H4><A NAME = "start_2"></A>2.2 Making LAMMPS
</H4>
<P>This section has the following sub-sections:
</P>
<UL><LI><A HREF = "#2_2_1">Read this first</A>
<LI><A HREF = "#2_2_2">Steps to build a LAMMPS executable</A>
<LI><A HREF = "#2_2_3">Common errors that can occur when making LAMMPS</A>
<LI><A HREF = "#2_2_4">Additional build tips</A>
<LI><A HREF = "#2_2_5">Building for a Mac</A>
<LI><A HREF = "#2_2_6">Building for Windows</A>
<UL><LI><A HREF = "#start_2_1">Read this first</A>
<LI><A HREF = "#start_2_2">Steps to build a LAMMPS executable</A>
<LI><A HREF = "#start_2_3">Common errors that can occur when making LAMMPS</A>
<LI><A HREF = "#start_2_4">Additional build tips</A>
<LI><A HREF = "#start_2_5">Building for a Mac</A>
<LI><A HREF = "#start_2_6">Building for Windows</A>
</UL>
<HR>
<A NAME = "2_2_1"></A><B><I>Read this first:</I></B>
<A NAME = "start_2_1"></A><B><I>Read this first:</I></B>
<P>Building LAMMPS can be non-trivial. You may need to edit a makefile,
there are compiler options to consider, additional libraries can be
@ -106,7 +106,7 @@ to the developers and we'll include it in future LAMMPS releases.
</P>
<HR>
<A NAME = "2_2_2"></A><B><I>Steps to build a LAMMPS executable:</I></B>
<A NAME = "start_2_2"></A><B><I>Steps to build a LAMMPS executable:</I></B>
<P><B>Step 0</B>
</P>
@ -129,7 +129,7 @@ will build LAMMPS more quickly.
produced, you're done; it's your lucky day.
</P>
<P>Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see <A HREF = "#2_3">this
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
section</A> below.
</P>
<P><B>Step 1</B>
@ -248,14 +248,15 @@ vendor-provided MPI which the compiler has no trouble finding.
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).
</P>
<P>If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
or 2.0 or OpenMPI. MPICH can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI
site</A>. OpenMPI can be downloaded the
<A HREF = "http://www.open-mpi.org">OpenMPI site</A>. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the
vendor should have already installed a version of MPI, which will be
faster than MPICH or OpenMPI or LAM, so find out how to build and link
with it. If you use MPICH or OpenMPI or LAM, you will have to
<P>If you are installing MPI yourself, we recommend Argonne's MPICH2
or OpenMPI. MPICH can be downloaded from the <A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/">Argonne MPI
site</A>. OpenMPI can
be downloaded from the <A HREF = "http://www.open-mpi.org">OpenMPI site</A>.
Other MPI packages should also work. If you are running on a big
parallel platform, your system people or the vendor should have
already installed a version of MPI, which is likely to be faster
than a self-installed MPICH or OpenMPI, so find out how to build
and link with it. If you use MPICH or OpenMPI, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
@ -329,7 +330,7 @@ truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT packages.
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
</P>
<P><B>Step 7</B>
</P>
@ -350,7 +351,7 @@ your machine, you may not need to set these variables.
<P><B>Step 8</B>
</P>
<P>Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see <A HREF = "#2_3">this
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
section</A> below, before proceeding to Step 9.
</P>
<P><B>Step 9</B>
@ -369,7 +370,7 @@ gmake foo
</P>
<HR>
<A NAME = "2_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>
<A NAME = "start_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>
<P>IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
@ -407,7 +408,7 @@ above in Step 4.
</P>
<HR>
<A NAME = "2_2_4"></A><B><I>Additional build tips:</I></B>
<A NAME = "start_2_4"></A><B><I>Additional build tips:</I></B>
<P>(1) Building LAMMPS for multiple platforms.
</P>
@ -462,18 +463,18 @@ secs/timestep.
</P>
<HR>
<A NAME = "2_2_5"></A><B><I>Building for a Mac:</I></B>
<A NAME = "start_2_5"></A><B><I>Building for a Mac:</I></B>
<P>OS X is BSD Unix, so it should just work. See the Makefile.mac file.
</P>
<HR>
<A NAME = "2_2_6"></A><B><I>Building for Windows:</I></B>
<A NAME = "start_2_6"></A><B><I>Building for Windows:</I></B>
<P>The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows exeutable. See the <A HREF = "#2_5">Running LAMMPS</A>
section for instructions for running these executables on a Windows
box.
parallel pre-built Windows exeutable. See the <A HREF = "#start_5">Running
LAMMPS</A> section for instructions for running these
executables on a Windows box.
</P>
<P>If the pre-built executable doesn't have the options you want, then
you can build LAMMPS from its source files on a Windows box. One way
@ -498,72 +499,63 @@ and USER-REAXC. The fourth project includes the USER-AWPMD package.
</P>
<HR>
<H4><A NAME = "2_3"></A>2.3 Making LAMMPS with optional packages
<H4><A NAME = "start_3"></A>2.3 Making LAMMPS with optional packages
</H4>
<P>This section has the following sub-sections:
</P>
<UL><LI><A HREF = "#2_3_1">Package basics</A>
<LI><A HREF = "#2_3_2">Including/excluding packages</A>
<LI><A HREF = "#2_3_3">Packages that require extra LAMMPS libraries</A>
<LI><A HREF = "#2_3_4">Additional Makefile settings for extra libraries</A>
<UL><LI><A HREF = "#start_3_1">Package basics</A>
<LI><A HREF = "#start_3_2">Including/excluding packages</A>
<LI><A HREF = "#start_3_3">Packages that require extra libraries</A>
<LI><A HREF = "#start_3_4">Additional Makefile settings for extra libraries</A>
</UL>
<HR>
<A NAME = "2_3_1"></A><B><I>Package basics:</I></B>
<A NAME = "start_3_1"></A><B><I>Package basics:</I></B>
<P>The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of all packages by typing "make package".
can see the list of all packages by typing "make package" from within
the src directory of the LAMMPS distribution.
</P>
<P>The current list of standard packages is as follows:
<P>If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command's doc page specfies if it is part of a
package. You can also type
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >asphere </TD><TD > aspherical particles and force fields</TD></TR>
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
<TR><TD >colloid </TD><TD > colloidal particle force fields</TD></TR>
<TR><TD >dipole </TD><TD > point dipole particles and force fields</TD></TR>
<TR><TD >dsmc </TD><TD > Direct Simulation Monte Carlo (DMSC) pair style</TD></TR>
<TR><TD >gpu </TD><TD > GPU-enabled force field styles</TD></TR>
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>
<TR><TD >manybody </TD><TD > metal, 3-body, bond-order potentials</TD></TR>
<TR><TD >meam </TD><TD > modified embedded atom method (MEAM) potential</TD></TR>
<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
<TR><TD >opt </TD><TD > optimized versions of a few pair potentials</TD></TR>
<TR><TD >peri </TD><TD > Peridynamics model and potential</TD></TR>
<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
<TR><TD >reax </TD><TD > ReaxFF potential</TD></TR>
<TR><TD >replica </TD><TD > multi-replica methods</TD></TR>
<TR><TD >shock </TD><TD > methods for MD simulations of shock loading</TD></TR>
<TR><TD >srd </TD><TD > stochastic rotation dynamics (SRD)</TD></TR>
<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
</TD></TR></TABLE></DIV>
<P>There are also several user-contributed packages which may be as
simple as a single additional file (see the src/USER-MISC directory)
or many files grouped together which add a specific functionality to
the code.
<PRE>lmp_machine -h
</PRE>
<P>to run your executable with the optional <A HREF = "#start_6">-h command-line
switch</A> for "help", which will list the styles and commands
known to your executable.
</P>
<P>The difference between a <I>standard</I> package versus a <I>user</I> package is
as follows:
<P>There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in <A HREF = "Section_packages.html">this section</A> of the manual. The
difference between standard and user packages is as follows:
</P>
<P>Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means we will answer questions about them, debug and fix them if
necessary, and keep them compatible with future changes to LAMMPS.
</P>
<P>User packages don't necessarily meet these requirements. If you have
problems using a feature provided in a user package, you will likely
need to contact the contributor directly to get help. Information on
how to submit additions you make to LAMMPS as a user-contributed
package is given in <A HREF = "Section_modify.html#package">this section</A> of the
documentation.
<P>User packages have been contributed by users, and always begin with
the user prefix. If they are a single command (single file), they are
typically in the user-misc package. Otherwise, they are a a set of
files grouped together which add a specific functionality to the code.
</P>
<P>User packages don't necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
package, you will likely need to contact the contributor directly to
get help. Information on how to submit additions you make to LAMMPS
as a user-contributed package is given in <A HREF = "Section_modify.html#mod_14">this
section</A> of the documentation.
</P>
<HR>
<A NAME = "2_3_2"></A><B><I>Including/excluding packages:</I></B>
<A NAME = "start_3_2"></A><B><I>Including/excluding packages:</I></B>
<P>To use or not use a package you must include or exclude it before
building LAMMPS. From the src directory, this is typically as simple
@ -588,15 +580,18 @@ of simulations. For some packages, this will keep you from having to
build auxiliary libraries (see below), and will also produce a smaller
executable which may run a bit faster.
</P>
<P>By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages.
<P>When you download a LAMMPS tarball, these packages are pre-installed
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
LAMMPS source files from the SVN or Git repositories, no packages are
pre-installed.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
"make yes-standard", "make no-standard", "make yes-user", "make
no-user", "make yes-all" or "make no-all" to include/exclude various
sets of packages. Type "make package" to see the all of the
package-related make options.
no-name", where "name" is the name of the package in lower-case, e.g.
name = kspace for the KSPACE package or name = user-atc for the
USER-ATC package. You can also type "make yes-standard", "make
no-standard", "make yes-user", "make no-user", "make yes-all" or "make
no-all" to include/exclude various sets of packages. Type "make
package" to see the all of the package-related make options.
</P>
<P>IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
@ -625,17 +620,18 @@ type "make package" to see all of the package-related make options.
</P>
<HR>
<A NAME = "2_3_3"></A><B><I>Packages that require extra LAMMPS libraries:</I></B>
<A NAME = "start_3_3"></A><B><I>Packages that require extra libraries:</I></B>
<P>A few of the standard and user packages require additional auxiliary
libraries be compiled first. If you get a LAMMPS build error about a
missing library, this is likely the reason. The source code for these
libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these.
libraries to be compiled first. If you get a LAMMPS build error about
a missing library, this is likely the reason. The source code for
these libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these or see
<A HREF = "Section_packages.html">this section</A> of the doc pages.
</P>
<P>Each lib directly has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done by
typing something like:
<P>Each lib directory has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done
in this manner:
</P>
<PRE>make -f Makefile.g++
</PRE>
@ -679,12 +675,12 @@ build will likely fail.
</P>
<HR>
<H4><A NAME = "2_4"></A>2.4 Building LAMMPS as a library
<H4><A NAME = "start_4"></A>2.4 Building LAMMPS as a library
</H4>
<P>LAMMPS itself can be built as a library, which can then be called from
another application or a scripting language. See <A HREF = "Section_howto.html#4_10">this
section</A> for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
another application or a scripting language. See <A HREF = "Section_howto.html#howto_10">this
section</A> for more info on coupling LAMMPS
to other codes. Building LAMMPS as a library is done by typing
</P>
<PRE>make makelib
make -f Makefile.lib foo
@ -710,19 +706,19 @@ src/library.cpp and src/library.h.
<P>See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in <A HREF = "Section_howto.html#4_10">this section</A> of the manual.
discussed in <A HREF = "Section_howto.html#howto_10">this section</A> of the manual.
See <A HREF = "Section_python.html">this section</A> of the manual for a description
of 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
for a description of the interface and how to extend it for your
needs.
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">this section</A> of the
manual for a description of the interface and how to extend it for
your needs.
</P>
<HR>
<H4><A NAME = "2_5"></A>2.5 Running LAMMPS
<H4><A NAME = "start_5"></A>2.5 Running LAMMPS
</H4>
<P>By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
@ -832,7 +828,7 @@ more processors or setup a smaller problem.
</P>
<HR>
<H4><A NAME = "2_6"></A>2.6 Command-line options
<H4><A NAME = "start_6"></A>2.6 Command-line options
</H4>
<P>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
@ -861,13 +857,13 @@ mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
</PRE>
<P>Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. If LAMMPS is built with this package, as described
above in <A HREF = "#2_3">Section 2.3</A>, then by default LAMMPS will run in CUDA
mode. If this switch is set to "off", then it will not, even if it
was built with the USER-CUDA package, which means you can run standard
LAMMPS or with the GPU package for testing or benchmarking purposes.
The only reason to set the switch to "on", is to check if LAMMPS was
built with the USER-CUDA package, since an error will be generated if
it was not.
above in <A HREF = "#start_3">Section 2.3</A>, then by default LAMMPS will run in
CUDA mode. If this switch is set to "off", then it will not, even if
it was built with the USER-CUDA package, which means you can run
standard LAMMPS or with the GPU package for testing or benchmarking
purposes. The only reason to set the switch to "on", is to check if
LAMMPS was built with the USER-CUDA package, since an error will be
generated if it was not.
</P>
<PRE>-echo style
</PRE>
@ -925,13 +921,13 @@ processors.
</P>
<P>Note that with MPI installed on a machine (e.g. your desktop), you can
run on more (virtual) processors than you have physical processors.
This can be useful for running <A HREF = "Section_howto.html#4_5">multi-replica
This can be useful for running <A HREF = "Section_howto.html#howto_5">multi-replica
simulations</A>, on one or a few processors.
</P>
<P>The input script specifies what simulation is run on which partition;
see the <A HREF = "variable.html">variable</A> and <A HREF = "next.html">next</A> commands. This
<A HREF = "Section_howto.html#4_4">howto section</A> gives examples of how to use
these commands in this way. Simulations running on different
<A HREF = "Section_howto.html#howto_4">howto section</A> gives examples of how to
use these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
<A HREF = "temper.html">temper</A> command.
</P>
@ -982,17 +978,18 @@ partition screen files file.N.
<PRE>-suffix style
</PRE>
<P>Use variants of various styles if they exist. The specified style can
be <I>opt</I> or <I>gpu</I> or <I>cuda</I>. These refer to optional packages that
LAMMPS can be built with, as described above in <A HREF = "#2_3">Section 2.3</A>.
The "opt" style corrsponds to the OPT package, the "gpu" style to the
GPU package, and the "cuda" style to the USER-CUDA package.
be <I>opt</I>, <I>omp</I>, <I>gpu</I>, or <I>cuda</I>. These refer to optional packages that
LAMMPS can be built with, as described above in <A HREF = "#start_3">Section
2.3</A>. The "opt" style corrsponds to the OPT package, the
"omp" style to the USER-OMP package, the "gpu" style to the GPU
package, and the "cuda" style to the USER-CUDA package.
</P>
<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
lj/cut</A> variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda. A variant styles can be specified
lj/cut</A> variant, with style names lj/cut/opt, lj/cut/omp,
lj/cut/gpu, or lj/cut/cuda. A variant styles can be specified
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
-suffix switch is used, you do not need to modify your input script.
The specified suffix (opt,gpu,cuda) is automatically appended whenever
The specified suffix (opt,omp,gpu,cuda) is automatically appended whenever
your input script command creates a new <A HREF = "atom_style.html">atom</A>,
<A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>, <A HREF = "compute.html">compute</A>, or
<A HREF = "run_style.html">run</A> style. atom, pair, fix, compute, or integrate
@ -1015,13 +1012,19 @@ value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the <A HREF = "variable.html">variable</A> command for more info on
defining index and other kinds of variables and <A HREF = "Section_commands.html#3_2">this
section</A> for more info on using variables in
input scripts.
defining index and other kinds of variables and <A HREF = "Section_commands.html#cmd_2">this
section</A> for more info on using variables
in input scripts.
</P>
<P>NOTE: Currently, the command-line parser looks for arguments that
start with "-" to indicate new switches. Thus you cannot specify
multiple variable values if any of they start with a "-", e.g. a
negative numeric value. It is OK if the first value1 starts with a
"-", since it is automatically skipped.
</P>
<HR>
<H4><A NAME = "2_7"></A>2.7 LAMMPS screen output
<H4><A NAME = "start_7"></A>2.7 LAMMPS screen output
</H4>
<P>As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
@ -1118,7 +1121,7 @@ communication, roughly 75% in the example above.
</P>
<HR>
<H4><A NAME = "2_8"></A>2.8 Tips for users of previous LAMMPS versions
<H4><A NAME = "start_8"></A>2.8 Tips for users of previous LAMMPS versions
</H4>
<P>The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed

251
doc/Section_start.txt
View File

@ -11,18 +11,18 @@
This section describes how to build and run LAMMPS, for both new and
experienced users.
2.1 "What's in the LAMMPS distribution"_#2_1
2.2 "Making LAMMPS"_#2_2
2.3 "Making LAMMPS with optional packages"_#2_3
2.4 "Building LAMMPS as a library"_#2_4
2.5 "Running LAMMPS"_#2_5
2.6 "Command-line options"_#2_6
2.7 "Screen output"_#2_7
2.8 "Tips for users of previous versions"_#2_8 :all(b)
2.1 "What's in the LAMMPS distribution"_#start_1
2.2 "Making LAMMPS"_#start_2
2.3 "Making LAMMPS with optional packages"_#start_3
2.4 "Building LAMMPS as a library"_#start_4
2.5 "Running LAMMPS"_#start_5
2.6 "Command-line options"_#start_6
2.7 "Screen output"_#start_7
2.8 "Tips for users of previous versions"_#start_8 :all(b)
:line
2.1 What's in the LAMMPS distribution :h4,link(2_1)
2.1 What's in the LAMMPS distribution :h4,link(start_1)
When you download LAMMPS you will need to unzip and untar the
downloaded file with the following commands, after placing the file in
@ -49,8 +49,8 @@ then you just get a single file:
lmp_windows.exe :pre
Skip to the "Running LAMMPS"_#2_5 sections for info on how to launch
these executables on a Windows box.
Skip to the "Running LAMMPS"_#start_5 sections for info on how to
launch these executables on a Windows box.
The Windows executables for serial or parallel only include certain
packages and bug-fixes/upgrades listed on "this
@ -62,20 +62,20 @@ as described in the next section.
:line
2.2 Making LAMMPS :h4,link(2_2)
2.2 Making LAMMPS :h4,link(start_2)
This section has the following sub-sections:
"Read this first"_#2_2_1
"Steps to build a LAMMPS executable"_#2_2_2
"Common errors that can occur when making LAMMPS"_#2_2_3
"Additional build tips"_#2_2_4
"Building for a Mac"_#2_2_5
"Building for Windows"_#2_2_6 :ul
"Read this first"_#start_2_1
"Steps to build a LAMMPS executable"_#start_2_2
"Common errors that can occur when making LAMMPS"_#start_2_3
"Additional build tips"_#start_2_4
"Building for a Mac"_#start_2_5
"Building for Windows"_#start_2_6 :ul
:line
[{Read this first:}] :link(2_2_1)
[{Read this first:}] :link(start_2_1)
Building LAMMPS can be non-trivial. You may need to edit a makefile,
there are compiler options to consider, additional libraries can be
@ -101,7 +101,7 @@ to the developers and we'll include it in future LAMMPS releases.
:line
[{Steps to build a LAMMPS executable:}] :link(2_2_2)
[{Steps to build a LAMMPS executable:}] :link(start_2_2)
[Step 0]
@ -125,7 +125,7 @@ produced, you're done; it's your lucky day.
Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see "this
section"_#2_3 below.
section"_#start_3 below.
[Step 1]
@ -243,14 +243,15 @@ Failing this, with these 3 variables you can specify where the mpi.h
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).
If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
or 2.0 or OpenMPI. MPICH can be downloaded from the "Argonne MPI
site"_http://www-unix.mcs.anl.gov/mpi. OpenMPI can be downloaded the
"OpenMPI site"_http://www.open-mpi.org. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the
vendor should have already installed a version of MPI, which will be
faster than MPICH or OpenMPI or LAM, so find out how to build and link
with it. If you use MPICH or OpenMPI or LAM, you will have to
If you are installing MPI yourself, we recommend Argonne's MPICH2
or OpenMPI. MPICH can be downloaded from the "Argonne MPI
site"_http://www.mcs.anl.gov/research/projects/mpich2/. OpenMPI can
be downloaded from the "OpenMPI site"_http://www.open-mpi.org.
Other MPI packages should also work. If you are running on a big
parallel platform, your system people or the vendor should have
already installed a version of MPI, which is likely to be faster
than a self-installed MPICH or OpenMPI, so find out how to build
and link with it. If you use MPICH or OpenMPI, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
@ -324,7 +325,7 @@ truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT packages.
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
[Step 7]
@ -346,7 +347,7 @@ your machine, you may not need to set these variables.
Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see "this
section"_#2_3 below, before proceeding to Step 9.
section"_#start_3 below, before proceeding to Step 9.
[Step 9]
@ -364,7 +365,7 @@ You should get the executable lmp_foo when the build is complete.
:line
[{Errors that can occur when making LAMMPS:}] :link(2_2_3)
[{Errors that can occur when making LAMMPS:}] :link(start_2_3)
IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
@ -402,7 +403,7 @@ above in Step 4.
:line
[{Additional build tips:}] :link(2_2_4)
[{Additional build tips:}] :link(start_2_4)
(1) Building LAMMPS for multiple platforms.
@ -457,18 +458,18 @@ secs/timestep.
:line
[{Building for a Mac:}] :link(2_2_5)
[{Building for a Mac:}] :link(start_2_5)
OS X is BSD Unix, so it should just work. See the Makefile.mac file.
:line
[{Building for Windows:}] :link(2_2_6)
[{Building for Windows:}] :link(start_2_6)
The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows exeutable. See the "Running LAMMPS"_#2_5
section for instructions for running these executables on a Windows
box.
parallel pre-built Windows exeutable. See the "Running
LAMMPS"_#start_5 section for instructions for running these
executables on a Windows box.
If the pre-built executable doesn't have the options you want, then
you can build LAMMPS from its source files on a Windows box. One way
@ -493,70 +494,63 @@ and USER-REAXC. The fourth project includes the USER-AWPMD package.
:line
2.3 Making LAMMPS with optional packages :h4,link(2_3)
2.3 Making LAMMPS with optional packages :h4,link(start_3)
This section has the following sub-sections:
"Package basics"_#2_3_1
"Including/excluding packages"_#2_3_2
"Packages that require extra LAMMPS libraries"_#2_3_3
"Additional Makefile settings for extra libraries"_#2_3_4 :ul
"Package basics"_#start_3_1
"Including/excluding packages"_#start_3_2
"Packages that require extra libraries"_#start_3_3
"Additional Makefile settings for extra libraries"_#start_3_4 :ul
:line
[{Package basics:}] :link(2_3_1)
[{Package basics:}] :link(start_3_1)
The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of all packages by typing "make package".
can see the list of all packages by typing "make package" from within
the src directory of the LAMMPS distribution.
The current list of standard packages is as follows:
If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command's doc page specfies if it is part of a
package. You can also type
asphere : aspherical particles and force fields
class2 : class 2 force fields
colloid : colloidal particle force fields
dipole : point dipole particles and force fields
dsmc : Direct Simulation Monte Carlo (DMSC) pair style
gpu : GPU-enabled force field styles
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers
manybody : metal, 3-body, bond-order potentials
meam : modified embedded atom method (MEAM) potential
molecule : force fields for molecular systems
opt : optimized versions of a few pair potentials
peri : Peridynamics model and potential
poems : coupled rigid body motion
reax : ReaxFF potential
replica : multi-replica methods
shock : methods for MD simulations of shock loading
srd : stochastic rotation dynamics (SRD)
xtc : dump atom snapshots in XTC format :tb(s=:)
lmp_machine -h :pre
There are also several user-contributed packages which may be as
simple as a single additional file (see the src/USER-MISC directory)
or many files grouped together which add a specific functionality to
the code.
to run your executable with the optional "-h command-line
switch"_#start_6 for "help", which will list the styles and commands
known to your executable.
The difference between a {standard} package versus a {user} package is
as follows:
There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in "this section"_Section_packages.html of the manual. The
difference between standard and user packages is as follows:
Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means we will answer questions about them, debug and fix them if
necessary, and keep them compatible with future changes to LAMMPS.
User packages don't necessarily meet these requirements. If you have
problems using a feature provided in a user package, you will likely
need to contact the contributor directly to get help. Information on
how to submit additions you make to LAMMPS as a user-contributed
package is given in "this section"_Section_modify.html#package of the
documentation.
User packages have been contributed by users, and always begin with
the user prefix. If they are a single command (single file), they are
typically in the user-misc package. Otherwise, they are a a set of
files grouped together which add a specific functionality to the code.
User packages don't necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
package, you will likely need to contact the contributor directly to
get help. Information on how to submit additions you make to LAMMPS
as a user-contributed package is given in "this
section"_Section_modify.html#mod_14 of the documentation.
:line
[{Including/excluding packages:}] :link(2_3_2)
[{Including/excluding packages:}] :link(start_3_2)
To use or not use a package you must include or exclude it before
building LAMMPS. From the src directory, this is typically as simple
@ -581,15 +575,18 @@ of simulations. For some packages, this will keep you from having to
build auxiliary libraries (see below), and will also produce a smaller
executable which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages.
When you download a LAMMPS tarball, these packages are pre-installed
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
LAMMPS source files from the SVN or Git repositories, no packages are
pre-installed.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
"make yes-standard", "make no-standard", "make yes-user", "make
no-user", "make yes-all" or "make no-all" to include/exclude various
sets of packages. Type "make package" to see the all of the
package-related make options.
no-name", where "name" is the name of the package in lower-case, e.g.
name = kspace for the KSPACE package or name = user-atc for the
USER-ATC package. You can also type "make yes-standard", "make
no-standard", "make yes-user", "make no-user", "make yes-all" or "make
no-all" to include/exclude various sets of packages. Type "make
package" to see the all of the package-related make options.
IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
@ -618,17 +615,18 @@ type "make package" to see all of the package-related make options.
:line
[{Packages that require extra LAMMPS libraries:}] :link(2_3_3)
[{Packages that require extra libraries:}] :link(start_3_3)
A few of the standard and user packages require additional auxiliary
libraries be compiled first. If you get a LAMMPS build error about a
missing library, this is likely the reason. The source code for these
libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these.
libraries to be compiled first. If you get a LAMMPS build error about
a missing library, this is likely the reason. The source code for
these libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these or see
"this section"_Section_packages.html of the doc pages.
Each lib directly has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done by
typing something like:
Each lib directory has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done
in this manner:
make -f Makefile.g++ :pre
@ -672,12 +670,12 @@ build will likely fail.
:line
2.4 Building LAMMPS as a library :h4,link(2_4)
2.4 Building LAMMPS as a library :h4,link(start_4)
LAMMPS itself can be built as a library, which can then be called from
another application or a scripting language. See "this
section"_Section_howto.html#4_10 for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
section"_Section_howto.html#howto_10 for more info on coupling LAMMPS
to other codes. Building LAMMPS as a library is done by typing
make makelib
make -f Makefile.lib foo :pre
@ -703,19 +701,19 @@ src/library.cpp and src/library.h.
See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in "this section"_Section_howto.html#4_10 of the manual.
discussed in "this section"_Section_howto.html#howto_10 of the manual.
See "this section"_Section_python.html of the manual for a description
of 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
for a description of the interface and how to extend it for your
needs.
to LAMMPS. See "this section"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
:line
2.5 Running LAMMPS :h4,link(2_5)
2.5 Running LAMMPS :h4,link(start_5)
By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
@ -822,7 +820,7 @@ more processors or setup a smaller problem.
:line
2.6 Command-line options :h4,link(2_6)
2.6 Command-line options :h4,link(start_6)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
@ -851,13 +849,13 @@ Here are the details on the options:
Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. If LAMMPS is built with this package, as described
above in "Section 2.3"_#2_3, then by default LAMMPS will run in CUDA
mode. If this switch is set to "off", then it will not, even if it
was built with the USER-CUDA package, which means you can run standard
LAMMPS or with the GPU package for testing or benchmarking purposes.
The only reason to set the switch to "on", is to check if LAMMPS was
built with the USER-CUDA package, since an error will be generated if
it was not.
above in "Section 2.3"_#start_3, then by default LAMMPS will run in
CUDA mode. If this switch is set to "off", then it will not, even if
it was built with the USER-CUDA package, which means you can run
standard LAMMPS or with the GPU package for testing or benchmarking
purposes. The only reason to set the switch to "on", is to check if
LAMMPS was built with the USER-CUDA package, since an error will be
generated if it was not.
-echo style :pre
@ -916,12 +914,12 @@ processors.
Note that with MPI installed on a machine (e.g. your desktop), you can
run on more (virtual) processors than you have physical processors.
This can be useful for running "multi-replica
simulations"_Section_howto.html#4_5, on one or a few processors.
simulations"_Section_howto.html#howto_5, on one or a few processors.
The input script specifies what simulation is run on which partition;
see the "variable"_variable.html and "next"_next.html commands. This
"howto section"_Section_howto.html#4_4 gives examples of how to use
these commands in this way. Simulations running on different
"howto section"_Section_howto.html#howto_4 gives examples of how to
use these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
"temper"_temper.html command.
@ -972,17 +970,18 @@ partition screen files file.N.
-suffix style :pre
Use variants of various styles if they exist. The specified style can
be {opt} or {gpu} or {cuda}. These refer to optional packages that
LAMMPS can be built with, as described above in "Section 2.3"_#2_3.
The "opt" style corrsponds to the OPT package, the "gpu" style to the
GPU package, and the "cuda" style to the USER-CUDA package.
be {opt}, {omp}, {gpu}, or {cuda}. These refer to optional packages that
LAMMPS can be built with, as described above in "Section
2.3"_#start_3. The "opt" style corrsponds to the OPT package, the
"omp" style to the USER-OMP package, the "gpu" style to the GPU
package, and the "cuda" style to the USER-CUDA package.
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda. A variant styles can be specified
lj/cut"_pair_lj.html variant, with style names lj/cut/opt, lj/cut/omp,
lj/cut/gpu, or lj/cut/cuda. A variant styles can be specified
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
-suffix switch is used, you do not need to modify your input script.
The specified suffix (opt,gpu,cuda) is automatically appended whenever
The specified suffix (opt,omp,gpu,cuda) is automatically appended whenever
your input script command creates a new "atom"_atom_style.html,
"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or
"run"_run_style.html style. atom, pair, fix, compute, or integrate
@ -1006,12 +1005,18 @@ variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the "variable"_variable.html command for more info on
defining index and other kinds of variables and "this
section"_Section_commands.html#3_2 for more info on using variables in
input scripts.
section"_Section_commands.html#cmd_2 for more info on using variables
in input scripts.
NOTE: Currently, the command-line parser looks for arguments that
start with "-" to indicate new switches. Thus you cannot specify
multiple variable values if any of they start with a "-", e.g. a
negative numeric value. It is OK if the first value1 starts with a
"-", since it is automatically skipped.
:line
2.7 LAMMPS screen output :h4,link(2_7)
2.7 LAMMPS screen output :h4,link(start_7)
As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
@ -1108,7 +1113,7 @@ communication, roughly 75% in the example above.
:line
2.8 Tips for users of previous LAMMPS versions :h4,link(2_8)
2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed

2
doc/Section_tools.html
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

BIN
doc/USER/sph/SPH_LAMMPS_userguide.pdf Executable file
View File

Binary file not shown.

2
doc/angle_charmm.html
View File

@ -49,7 +49,7 @@ internally; hence the units of K are in energy/radian^2.
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/angle_charmm.txt
View File

@ -46,8 +46,8 @@ internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

6
doc/angle_class2.html
View File

@ -80,9 +80,9 @@ same value from the Ea formula.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"class2" package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info on packages.
<P>This angle style can only be used if LAMMPS was built with the CLASS2
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>

6
doc/angle_class2.txt
View File

@ -77,9 +77,9 @@ same value from the Ea formula.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"class2" package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info on packages.
This angle style can only be used if LAMMPS was built with the CLASS2
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]

4
doc/angle_cmm.html
View File

@ -52,8 +52,8 @@ internally; hence the units of K are in energy/radian^2.
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"user-cg-cmm" package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section
for more info on packages.
USER-CG-CMM package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>

4
doc/angle_cmm.txt
View File

@ -49,8 +49,8 @@ internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"user-cg-cmm" package. See the "Making LAMMPS"_Section_start.html#2_3 section
for more info on packages.
USER-CG-CMM package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_coeff.html
View File

@ -81,7 +81,7 @@ specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command
</UL>
<P>There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>

2
doc/angle_coeff.txt
View File

@ -79,7 +79,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line

2
doc/angle_cosine.html
View File

@ -38,7 +38,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/angle_cosine.txt
View File

@ -35,8 +35,8 @@ K (energy) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_cosine_delta.html
View File

@ -43,7 +43,7 @@ internally.
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/angle_cosine_delta.txt
View File

@ -40,8 +40,8 @@ internally.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

10
doc/angle_cosine_periodic.html
View File

@ -23,10 +23,10 @@ angle_coeff * 75.0 1 6
<P><B>Description:</B>
</P>
<P>The <I>cosine/periodic</I> angle style uses the following potential, which
is commonly used in the <A HREF = "Section_howto.html#4_4">DREIDING</A> force field,
particularly for organometallic systems where <I>n</I> = 4 might be used
for an octahedral complex and <I>n</I> = 3 might be used for a trigonal
center:
is commonly used in the <A HREF = "Section_howto.html#howto_4">DREIDING</A> force
field, particularly for organometallic systems where <I>n</I> = 4 might be
used for an octahedral complex and <I>n</I> = 3 might be used for a
trigonal center:
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_periodic.jpg">
</CENTER>
@ -51,7 +51,7 @@ geometry.
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

12
doc/angle_cosine_periodic.txt
View File

@ -20,10 +20,10 @@ angle_coeff * 75.0 1 6 :pre
[Description:]
The {cosine/periodic} angle style uses the following potential, which
is commonly used in the "DREIDING"_Section_howto.html#4_4 force field,
particularly for organometallic systems where {n} = 4 might be used
for an octahedral complex and {n} = 3 might be used for a trigonal
center:
is commonly used in the "DREIDING"_Section_howto.html#howto_4 force
field, particularly for organometallic systems where {n} = 4 might be
used for an octahedral complex and {n} = 3 might be used for a
trigonal center:
:c,image(Eqs/angle_cosine_periodic.jpg)
@ -48,8 +48,8 @@ geometry.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_cosine_shift.html
View File

@ -41,7 +41,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"user-misc" package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>

2
doc/angle_cosine_shift.txt
View File

@ -38,7 +38,7 @@ theta (angle) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"user-misc" package. See the "Making LAMMPS"_Section_start.html#2_3
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]

2
doc/angle_cosine_shift_exp.html
View File

@ -53,7 +53,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"user-misc" package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>

2
doc/angle_cosine_shift_exp.txt
View File

@ -50,7 +50,7 @@ A (real number) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"user-misc" package. See the "Making LAMMPS"_Section_start.html#2_3
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]

2
doc/angle_cosine_squared.html
View File

@ -43,7 +43,7 @@ internally.
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/angle_cosine_squared.txt
View File

@ -40,8 +40,8 @@ internally.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_harmonic.html
View File

@ -43,7 +43,7 @@ internally; hence the units of K are in energy/radian^2.
<P><B>Restrictions:</B> none
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/angle_harmonic.txt
View File

@ -40,8 +40,8 @@ internally; hence the units of K are in energy/radian^2.
[Restrictions:] none
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

4
doc/angle_hybrid.html
View File

@ -74,10 +74,12 @@ in place of an angle style, either in a input script angle_coeff
command or in the data file, if you desire to turn off interactions
for specific angle types.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other angle styles, the hybrid angle style does not store angle

6
doc/angle_hybrid.txt
View File

@ -71,11 +71,13 @@ in place of an angle style, either in a input script angle_coeff
command or in the data file, if you desire to turn off interactions
for specific angle types.
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart

10
doc/angle_style.html
View File

@ -73,7 +73,7 @@ specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command
</UL>
<P>There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>
@ -83,10 +83,10 @@ page</A>.
<P>Angle styles can only be set for atom_styles that allow angles to be
defined.
</P>
<P>Most angle styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info on packages. The
doc pages for individual bond potentials tell if it is part of a
<P>Most angle styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
</P>
<P><B>Related commands:</B>

8
doc/angle_style.txt
View File

@ -72,7 +72,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line
@ -81,10 +81,10 @@ page"_Section_commands.html#3_5.
Angle styles can only be set for atom_styles that allow angles to be
defined.
Most angle styles are part of the "molecular" package. They are only
Most angle styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual bond potentials tell if it is part of a
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
[Related commands:]

2
doc/angle_table.html
View File

@ -124,7 +124,7 @@ one that matches the specified keyword.
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/angle_table.txt
View File

@ -121,8 +121,8 @@ one that matches the specified keyword.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

40
doc/atom_style.html
View File

@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
@ -61,9 +61,12 @@ quantities.
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
<TR><TD ><I>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
</TD></TR></TABLE></DIV>
@ -72,8 +75,8 @@ the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
</P>
<P>All of the styles define point particles, except the <I>sphere</I>,
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, and <I>wavepacket</I> styles, which define
finite-size particles.
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, and <I>tri</I>
styles, which define finite-size particles.
</P>
<P>For the <I>sphere</I> style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
@ -93,12 +96,24 @@ position, which is represented by the eradius = electron size.
<P>For the <I>peri</I> style, the particles are spherical and each stores a
per-particle mass and volume.
</P>
<P>The <I>meso</I> style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
</P>
<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical <I>etag</I> values.
</P>
<P>For the <I>line</I> style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
</P>
<P>For the <I>tri</I> style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
</P>
<HR>
<P>Typically, simulations require only a single (non-hybrid) atom style.
@ -124,15 +139,16 @@ section</A>.
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
"molecular" package. The <I>dipole</I> style is part of the "dipole"
package. The <I>ellipsoid</I> style is part of the "asphere" package. The
<I>peri</I> style is part of the "peri" package for Peridynamics. The
<I>electron</I> style is part of the "user-eff" package for <A HREF = "pair_eff.html">electronic
force fields</A>. The <I>wavepacket</I> style is part of the
"user-awpmd" package for the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD
method</A>. They are only enabled if LAMMPS was built
with that package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
MOLECULAR package. The <I>dipole</I> style is part of the "dipole"
package. The <I>peri</I> style is part of the PERI package for
Peridynamics. The <I>electron</I> style is part of the USER-EFF package
for <A HREF = "pair_eff.html">electronic force fields</A>. The <I>meso</I> style is part
of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
LAMMPS. The <I>wavepacket</I> style is part of the USER-AWPMD package for
the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

42
doc/atom_style.txt
View File

@ -13,8 +13,8 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
{electron} or {ellipsoid} or {full} or {molecular} or \
{peri} or {sphere} or {hybrid} :ul
{electron} or {ellipsoid} or {full} or {line} or {meso} or \
{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -58,9 +58,12 @@ quantities.
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{sphere} | diameter, mass, angular velocity | granular models |
{tri} | corner points, angular momentum | rigid bodies |
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
All of the styles assign mass to particles on a per-type basis, using
@ -68,8 +71,8 @@ the "mass"_mass.html command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
All of the styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, and {wavepacket} styles, which define
finite-size particles.
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, and {tri}
styles, which define finite-size particles.
For the {sphere} style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
@ -89,12 +92,24 @@ position, which is represented by the eradius = electron size.
For the {peri} style, the particles are spherical and each stores a
per-particle mass and volume.
The {meso} style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical {etag} values.
For the {line} style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
:line
Typically, simulations require only a single (non-hybrid) atom style.
@ -120,15 +135,16 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The {angle}, {bond}, {full}, and {molecular} styles are part of the
"molecular" package. The {dipole} style is part of the "dipole"
package. The {ellipsoid} style is part of the "asphere" package. The
{peri} style is part of the "peri" package for Peridynamics. The
{electron} style is part of the "user-eff" package for "electronic
force fields"_pair_eff.html. The {wavepacket} style is part of the
"user-awpmd" package for the "antisymmetrized wave packet MD
method"_pair_awpmd.html. They are only enabled if LAMMPS was built
with that package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
MOLECULAR package. The {dipole} style is part of the "dipole"
package. The {peri} style is part of the PERI package for
Peridynamics. The {electron} style is part of the USER-EFF package
for "electronic force fields"_pair_eff.html. The {meso} style is part
of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for
the "antisymmetrized wave packet MD method"_pair_awpmd.html. They are
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

6
doc/bond_class2.html
View File

@ -42,9 +42,9 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the "class2"
package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
more info on packages.
<P>This bond style can only be used if LAMMPS was built with the CLASS2
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>

6
doc/bond_class2.txt
View File

@ -39,9 +39,9 @@ K4 (energy/distance^4) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the "class2"
package. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info on packages.
This bond style can only be used if LAMMPS was built with the CLASS2
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]

2
doc/bond_coeff.html
View File

@ -77,7 +77,7 @@ specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</UL>
<P>There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>

2
doc/bond_coeff.txt
View File

@ -75,7 +75,7 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line

2
doc/bond_fene.html
View File

@ -45,7 +45,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>

4
doc/bond_fene.txt
View File

@ -42,8 +42,8 @@ sigma (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
You typically should specify "special_bonds fene"_special_bonds.html"
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond

2
doc/bond_fene_expand.html
View File

@ -50,7 +50,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>

4
doc/bond_fene_expand.txt
View File

@ -47,8 +47,8 @@ delta (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
You typically should specify "special_bonds fene"_special_bonds.html"
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond

2
doc/bond_harmonic.html
View File

@ -40,7 +40,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/bond_harmonic.txt
View File

@ -37,8 +37,8 @@ r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/bond_harmonic_shift.html
View File

@ -45,7 +45,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"user-misc" package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>

2
doc/bond_harmonic_shift.txt
View File

@ -40,7 +40,7 @@ rc (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"user-misc" package. See the "Making LAMMPS"_Section_start.html#2_3
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]

2
doc/bond_harmonic_shift_cut.html
View File

@ -43,7 +43,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"user-misc" package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>

2
doc/bond_harmonic_shift_cut.txt
View File

@ -40,7 +40,7 @@ rc (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"user-misc" package. See the "Making LAMMPS"_Section_start.html#2_3
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]

4
doc/bond_hybrid.html
View File

@ -57,10 +57,12 @@ place of a bond style, either in a input script bond_coeff command or
in the data file, if you desire to turn off interactions for specific
bond types.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other bond styles, the hybrid bond style does not store bond

6
doc/bond_hybrid.txt
View File

@ -54,11 +54,13 @@ place of a bond style, either in a input script bond_coeff command or
in the data file, if you desire to turn off interactions for specific
bond types.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart

2
doc/bond_morse.html
View File

@ -41,7 +41,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/bond_morse.txt
View File

@ -38,8 +38,8 @@ r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/bond_nonlinear.html
View File

@ -41,7 +41,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/bond_nonlinear.txt
View File

@ -38,8 +38,8 @@ lamda (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/bond_quartic.html
View File

@ -76,7 +76,7 @@ delete_bonds all bond 0 remove
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>The <I>quartic</I> style requires that <A HREF = "special_bonds.html">special_bonds</A>

4
doc/bond_quartic.txt
View File

@ -73,8 +73,8 @@ delete_bonds all bond 0 remove :pre
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,

10
doc/bond_style.html
View File

@ -82,7 +82,7 @@ specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</UL>
<P>There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>
@ -92,10 +92,10 @@ page</A>.
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>Most bond styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info on packages. The
doc pages for individual bond potentials tell if it is part of a
<P>Most bond styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
</P>
<P><B>Related commands:</B>

8
doc/bond_style.txt
View File

@ -80,7 +80,7 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line
@ -89,10 +89,10 @@ page"_Section_commands.html#3_5.
Bond styles can only be set for atom styles that allow bonds to be
defined.
Most bond styles are part of the "molecular" package. They are only
Most bond styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual bond potentials tell if it is part of a
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
[Related commands:]

2
doc/bond_table.html
View File

@ -121,7 +121,7 @@ one that matches the specified keyword.
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>

4
doc/bond_table.txt
View File

@ -118,8 +118,8 @@ one that matches the specified keyword.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

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