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@ -122,49 +122,67 @@ it gives quick access to documentation for all LAMMPS commands.
<BR>
3.5 <A HREF = "Section_commands.html#3_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_commands.html#3_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_commands.html#3_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Using accelerated CPU and GPU styles</A>
<UL> 5.1 <A HREF = "Section_howto.html#4_1">OPT package</A>
<BR>
5.2 <A HREF = "Section_howto.html#4_2">USER-OMP package</A>
<BR>
5.3 <A HREF = "Section_howto.html#4_3">GPU package</A>
<BR>
5.4 <A HREF = "Section_howto.html#4_4">USER-CUDA package</A>
<BR>
5.5 <A HREF = "Section_howto.html#4_5">Comparison of GPU and USER-CUDA packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 4.1 <A HREF = "Section_howto.html#4_1">Restarting a simulation</A>
<UL> 6.1 <A HREF = "Section_commands.html#4_1">Restarting a simulation</A>
<BR>
4.2 <A HREF = "Section_howto.html#4_2">2d simulations</A>
6.2 <A HREF = "Section_commands.html#4_2">2d simulations</A>
<BR>
4.3 <A HREF = "Section_howto.html#4_3">CHARMM and AMBER force fields</A>
6.3 <A HREF = "4_3">CHARMM and AMBER force fields</A>
<BR>
4.4 <A HREF = "Section_howto.html#4_4">Running multiple simulations from one input script</A>
6.4 <A HREF = "4_4">Running multiple simulations from one input script</A>
<BR>
4.5 <A HREF = "Section_howto.html#4_5">Multi-replica simulations</A>
6.5 <A HREF = "4_5">Multi-replica simulations</A>
<BR>
4.6 <A HREF = "Section_howto.html#4_6">Granular models</A>
6.6 <A HREF = "4_6">Granular models</A>
<BR>
4.7 <A HREF = "Section_howto.html#4_7">TIP3P water model</A>
6.7 <A HREF = "4_7">TIP3P water model</A>
<BR>
4.8 <A HREF = "Section_howto.html#4_8">TIP4P water model</A>
6.8 <A HREF = "4_8">TIP4P water model</A>
<BR>
4.9 <A HREF = "Section_howto.html#4_9">SPC water model</A>
6.9 <A HREF = "4_9">SPC water model</A>
<BR>
4.10 <A HREF = "Section_howto.html#4_10">Coupling LAMMPS to other codes</A>
6.10 <A HREF = "4_10">Coupling LAMMPS to other codes</A>
<BR>
4.11 <A HREF = "Section_howto.html#4_11">Visualizing LAMMPS snapshots</A>
6.11 <A HREF = "4_11">Visualizing LAMMPS snapshots</A>
<BR>
4.12 <A HREF = "Section_howto.html#4_12">Triclinic (non-orthogonal) simulation boxes</A>
6.12 <A HREF = "4_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
4.13 <A HREF = "Section_howto.html#4_13">NEMD simulations</A>
6.13 <A HREF = "4_13">NEMD simulations</A>
<BR>
4.14 <A HREF = "Section_howto.html#4_14">Extended spherical and aspherical particles</A>
6.14 <A HREF = "4_14">Extended spherical and aspherical particles</A>
<BR>
4.15 <A HREF = "Section_howto.html#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
6.15 <A HREF = "4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
4.16 <A HREF = "Section_howto.html#4_16">Thermostatting, barostatting, and compute temperature</A>
6.16 <A HREF = "4_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
4.17 <A HREF = "Section_howto.html#4_17">Walls</A>
6.17 <A HREF = "4_17">Walls</A>
<BR>
4.18 <A HREF = "Section_howto.html#4_18">Elastic constants</A>
6.18 <A HREF = "4_18">Elastic constants</A>
<BR>
4.19 <A HREF = "Section_howto.html#4_19">Library interface to LAMMPS</A>
6.19 <A HREF = "4_19">Library interface to LAMMPS</A>
<BR>
4.20 <A HREF = "Section_howto.html#4_20">Calculating thermal conductivity</A>
6.20 <A HREF = "4_20">Calculating thermal conductivity</A>
<BR>
4.21 <A HREF = "Section_howto.html#4_21">Calculating viscosity</A>
6.21 <A HREF = "4_21">Calculating viscosity</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
@ -174,45 +192,63 @@ it gives quick access to documentation for all LAMMPS commands.
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_howto.html#4_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_howto.html#4_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_howto.html#4_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_howto.html#4_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_howto.html#4_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_howto.html#4_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_howto.html#4_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_howto.html#4_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_howto.html#4_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_howto.html#10_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_howto.html#10_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_howto.html#4_12">Thermodynamic output options</A>
<BR>
10.13 <A HREF = "Section_howto.html#4_13">Variable options</A>
<BR>
10.14 <A HREF = "Section_howto.html#4_14">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 9.1 <A HREF = "Section_python.html#9_1">Extending Python with a serial version of LAMMPS</A>
<UL> 11.1 <A HREF = "9_1">Extending Python with a serial version of LAMMPS</A>
<BR>
9.2 <A HREF = "Section_python.html#9_2">Creating a shared MPI library</A>
11.2 <A HREF = "9_2">Creating a shared MPI library</A>
<BR>
9.3 <A HREF = "Section_python.html#9_3">Extending Python with a parallel version of LAMMPS</A>
11.3 <A HREF = "9_3">Extending Python with a parallel version of LAMMPS</A>
<BR>
9.4 <A HREF = "Section_python.html#9_4">Extending Python with MPI</A>
11.4 <A HREF = "9_4">Extending Python with MPI</A>
<BR>
9.5 <A HREF = "Section_python.html#9_5">Testing the Python-LAMMPS interface</A>
11.5 <A HREF = "9_5">Testing the Python-LAMMPS interface</A>
<BR>
9.6 <A HREF = "Section_python.html#9_6">Using LAMMPS from Python</A>
11.6 <A HREF = "9_6">Using LAMMPS from Python</A>
<BR>
9.7 <A HREF = "Section_python.html#9_7">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Using accelerated CPU and GPU styles</A>
<UL> 10.1 <A HREF = "Section_accelerate.html#10_1">OPT package</A>
<BR>
10.2 <A HREF = "Section_accelerate.html#10_2">GPU package</A>
<BR>
10.3 <A HREF = "Section_accelerate.html#10_3">USER-CUDA package</A>
<BR>
10.4 <A HREF = "Section_accelerate.html#10_4">Comparison of GPU and USER-CUDA packages</A>
11.7 <A HREF = "9_7">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 11.1 <A HREF = "Section_errors.html#11_1">Common problems</A>
<UL> 12.1 <A HREF = "Section_python.html#9_1">Common problems</A>
<BR>
11.2 <A HREF = "Section_errors.html#11_2">Reporting bugs</A>
12.2 <A HREF = "Section_python.html#9_2">Reporting bugs</A>
<BR>
11.3 <A HREF = "Section_errors.html#11_3">Error & warning messages</A>
12.3 <A HREF = "Section_python.html#9_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 12.1 <A HREF = "Section_history.html#12_1">Coming attractions</A>
<UL> 13.1 <A HREF = "Section_errors.html#11_1">Coming attractions</A>
<BR>
12.2 <A HREF = "Section_history.html#12_2">Past versions</A>
13.2 <A HREF = "Section_errors.html#11_2">Past versions</A>
<BR></UL>
</OL>
@ -305,6 +341,40 @@ it gives quick access to documentation for all LAMMPS commands.