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19 +- doc/prd.txt | 19 +- doc/processors.html | 6 +- doc/processors.txt | 4 +- doc/read_data.html | 4 +- doc/read_data.txt | 4 +- doc/suffix.html | 10 +- doc/suffix.txt | 8 +- doc/tad.html | 4 +- doc/tad.txt | 4 +- doc/temper.html | 18 +- doc/temper.txt | 18 +- doc/variable.html | 12 +- doc/variable.txt | 12 +- 308 files changed, 1151 insertions(+), 1121 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index 27fd5eb36f..bcb1500514 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -82,107 +82,107 @@ it gives quick access to documentation for all LAMMPS commands.

  1. Introduction -
diff --git a/doc/Manual.txt b/doc/Manual.txt index 1a8107aee2..2b645ae715 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -77,172 +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"_3_1 :ulb,b - 4.2 "User packages"_3_2 :ule,b + 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"_10_1 :ulb,b - 5.2 "USER-OMP package"_10_2 :b - 5.3 "GPU package"_10_3 :b - 5.4 "USER-CUDA package"_10_4 :b - 5.5 "Comparison of GPU and USER-CUDA packages"_10_5 :ule,b + 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 - 6.1 "Restarting a simulation"_4_1 :ulb,b - 6.2 "2d simulations"_4_2 :b - 6.3 "CHARMM and AMBER force fields"_4_3 :b - 6.4 "Running multiple simulations from one input script"_4_4 :b - 6.5 "Multi-replica simulations"_4_5 :b - 6.6 "Granular models"_4_6 :b - 6.7 "TIP3P water model"_4_7 :b - 6.8 "TIP4P water model"_4_8 :b - 6.9 "SPC water model"_4_9 :b - 6.10 "Coupling LAMMPS to other codes"_4_10 :b - 6.11 "Visualizing LAMMPS snapshots"_4_11 :b - 6.12 "Triclinic (non-orthogonal) simulation boxes"_4_12 :b - 6.13 "NEMD simulations"_4_13 :b - 6.14 "Extended spherical and aspherical particles"_4_14 :b - 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_4_15 :b - 6.16 "Thermostatting, barostatting, and compute temperature"_4_16 :b - 6.17 "Walls"_4_17 :b - 6.18 "Elastic constants"_4_18 :b - 6.19 "Library interface to LAMMPS"_4_19 :b - 6.20 "Calculating thermal conductivity"_4_20 :b - 6.21 "Calculating viscosity"_4_21 :ule,b + 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"_10_1 :ulb,b - 10.2 "Bond, angle, dihedral, improper potentials"_10_2 :b - 10.3 "Compute styles"_10_3 :b - 10.4 "Dump styles"_10_4 :b - 10.5 "Dump custom output options"_10_5 :b - 10.6 "Fix styles"_10_6 :b - 10.7 "Input script commands"_10_7 :b - 10.8 "Kspace computations"_10_8 :b - 10.9 "Minimization styles"_10_9 :b - 10.10 "Pairwise potentials"_10_10 :b - 10.11 "Region styles"_10_11 :b - 10.12 "Thermodynamic output options"_10_12 :b - 10.13 "Variable options"_10_13 :b - 10.14 "Submitting new features for inclusion in LAMMPS"_10_14 :ule,b + 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 - 11.1 "Extending Python with a serial version of LAMMPS"_9_1 :ulb,b - 11.2 "Creating a shared MPI library"_9_2 :b - 11.3 "Extending Python with a parallel version of LAMMPS"_9_3 :b - 11.4 "Extending Python with MPI"_9_4 :b - 11.5 "Testing the Python-LAMMPS interface"_9_5 :b - 11.6 "Using LAMMPS from Python"_9_6 :b - 11.7 "Example Python scripts that use LAMMPS"_9_7 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+:link(py_2,Section_python.html#py_2) +:link(py_3,Section_python.html#py_3) +:link(py_4,Section_python.html#py_4) +:link(py_5,Section_python.html#py_5) +:link(py_6,Section_python.html#py_6) +:link(py_7,Section_python.html#py_7) -:link(12_1,Section_errors.html#11_1) -:link(12_2,Section_errors.html#11_2) -:link(12_3,Section_errors.html#11_3) +:link(err_1,Section_errors.html#err_1) +:link(err_2,Section_errors.html#err_2) +:link(err_3,Section_errors.html#err_3) -:link(13_1,Section_history.html#12_1) -:link(13_2,Section_history.html#12_2) +:link(hist_1,Section_history.html#hist_1) +:link(hist_2,Section_history.html#hist_2) diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index 4e279faf23..c314ea830b 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -36,7 +36,7 @@ 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 +script. Or you can use the -suffix command-line switch to invoke the accelerated versions automatically, without changing your input script. The suffix command allows you to set a suffix explicitly and @@ -164,10 +164,10 @@ hardware and install specific NVIDIA CUDA software on your system:

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 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 this +section 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
@@ -201,7 +201,7 @@ and in many cases it will be more efficient to run this way.