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@ -82,107 +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_commands.html#3_1">Standard packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_commands.html#3_2">User packages</A>
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_howto.html#4_1">OPT package</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">OPT package</A>
<BR>
5.2 <A HREF = "Section_howto.html#4_2">USER-OMP package</A>
5.2 <A HREF = "Section_accelerate.html#acc_2">USER-OMP package</A>
<BR>
5.3 <A HREF = "Section_howto.html#4_3">GPU package</A>
5.3 <A HREF = "Section_accelerate.html#acc_3">GPU package</A>
<BR>
5.4 <A HREF = "Section_howto.html#4_4">USER-CUDA package</A>
5.4 <A HREF = "Section_accelerate.html#acc_4">USER-CUDA package</A>
<BR>
5.5 <A HREF = "Section_howto.html#4_5">Comparison of GPU and USER-CUDA packages</A>
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> 6.1 <A HREF = "Section_commands.html#4_1">Restarting a simulation</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_commands.html#4_2">2d simulations</A>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "4_3">CHARMM and AMBER force fields</A>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "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>
6.5 <A HREF = "4_5">Multi-replica simulations</A>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "4_6">Granular models</A>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "4_7">TIP3P water model</A>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "4_8">TIP4P water model</A>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "4_9">SPC water model</A>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "4_10">Coupling LAMMPS to other codes</A>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "4_11">Visualizing LAMMPS snapshots</A>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "4_12">Triclinic (non-orthogonal) simulation boxes</A>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "4_13">NEMD simulations</A>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "4_14">Extended spherical and aspherical particles</A>
6.14 <A HREF = "Section_howto.html#howto_14">Extended spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "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>
6.16 <A HREF = "4_16">Thermostatting, barostatting, and compute temperature</A>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "4_17">Walls</A>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "4_18">Elastic constants</A>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "4_19">Library interface to LAMMPS</A>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "4_20">Calculating thermal conductivity</A>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "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>
@ -192,63 +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>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_howto.html#4_2">Bond, angle, dihedral, improper potentials</A>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_howto.html#4_3">Compute styles</A>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_howto.html#4_4">Dump styles</A>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_howto.html#4_5">Dump custom output options</A>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_howto.html#4_6">Fix styles</A>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_howto.html#4_7">Input script commands</A>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_howto.html#4_8">Kspace computations</A>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_howto.html#4_9">Minimization styles</A>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_howto.html#10_10">Pairwise potentials</A>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_howto.html#10_11">Region styles</A>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_howto.html#4_12">Thermodynamic output options</A>
10.12 <A HREF = "Section_modify.html#mod_12">Thermodynamic output options</A>
<BR>
10.13 <A HREF = "Section_howto.html#4_13">Variable options</A>
10.13 <A HREF = "Section_modify.html#mod_13">Variable options</A>
<BR>
10.14 <A HREF = "Section_howto.html#4_14">Submitting new features for inclusion in LAMMPS</A>
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> 11.1 <A HREF = "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>
11.2 <A HREF = "9_2">Creating a shared MPI library</A>
11.2 <A HREF = "Section_python.html#py_2">Creating a shared MPI library</A>
<BR>
11.3 <A HREF = "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>
11.4 <A HREF = "9_4">Extending Python with MPI</A>
11.4 <A HREF = "Section_python.html#py_4">Extending Python with MPI</A>
<BR>
11.5 <A HREF = "9_5">Testing the Python-LAMMPS interface</A>
11.5 <A HREF = "Section_python.html#py_5">Testing the Python-LAMMPS interface</A>
<BR>
11.6 <A HREF = "9_6">Using LAMMPS from Python</A>
11.6 <A HREF = "Section_python.html#py_6">Using LAMMPS from Python</A>
<BR>
11.7 <A HREF = "9_7">Example Python scripts that use LAMMPS</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> 12.1 <A HREF = "Section_python.html#9_1">Common problems</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_python.html#9_2">Reporting bugs</A>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_python.html#9_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> 13.1 <A HREF = "Section_errors.html#11_1">Coming attractions</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_errors.html#11_2">Past versions</A>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>

286
doc/Manual.txt
View File

@ -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
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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
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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 :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
12.1 "Common problems"_11_1 :ulb,b
12.2 "Reporting bugs"_11_2 :b
12.3 "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
13.1 "Coming attractions"_12_1 :ulb,b
13.2 "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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:link(start_2,Section_start.html#start_2)
:link(start_3,Section_start.html#start_3)
:link(start_4,Section_start.html#start_4)
:link(start_5,Section_start.html#start_5)
:link(start_6,Section_start.html#start_6)
:link(start_7,Section_start.html#start_7)
:link(start_8,Section_start.html#start_8)
:link(3_1,Section_commands.html#3_1)
:link(3_2,Section_commands.html#3_2)
:link(3_3,Section_commands.html#3_3)
:link(3_4,Section_commands.html#3_4)
:link(3_5,Section_commands.html#3_5)
:link(cmd_1,Section_commands.html#cmd_1)
:link(cmd_2,Section_commands.html#cmd_2)
:link(cmd_3,Section_commands.html#cmd_3)
:link(cmd_4,Section_commands.html#cmd_4)
:link(cmd_5,Section_commands.html#cmd_5)
:link(4_1,Section_commands.html#4_1)
:link(4_2,Section_commands.html#4_2)
:link(pkg_1,Section_packages.html#pkg_1)
:link(pkg_2,Section_packages.html#pkg_2)
:link(5_1,Section_commands.html#4_1)
:link(5_2,Section_commands.html#4_2)
:link(5_3,Section_commands.html#4_2)
:link(5_4,Section_commands.html#4_2)
:link(5_5,Section_commands.html#4_2)
:link(acc_1,Section_accelerate.html#acc_1)
:link(acc_2,Section_accelerate.html#acc_2)
:link(acc_3,Section_accelerate.html#acc_3)
:link(acc_4,Section_accelerate.html#acc_4)
:link(acc_5,Section_accelerate.html#acc_5)
:link(6_1,Section_howto.html#4_1)
:link(6_2,Section_howto.html#4_2)
:link(6_3,Section_howto.html#4_3)
:link(6_4,Section_howto.html#4_4)
:link(6_5,Section_howto.html#4_5)
:link(6_6,Section_howto.html#4_6)
:link(6_7,Section_howto.html#4_7)
:link(6_8,Section_howto.html#4_8)
:link(6_9,Section_howto.html#4_9)
:link(6_10,Section_howto.html#6_10)
:link(6_11,Section_howto.html#6_11)
:link(6_12,Section_howto.html#4_12)
:link(6_13,Section_howto.html#4_13)
:link(6_14,Section_howto.html#4_14)
:link(6_15,Section_howto.html#4_15)
:link(6_16,Section_howto.html#4_16)
:link(6_17,Section_howto.html#4_17)
:link(6_18,Section_howto.html#4_18)
:link(6_19,Section_howto.html#4_19)
:link(6_20,Section_howto.html#4_20)
:link(6_21,Section_howto.html#4_21)
:link(howto_1,Section_howto.html#howto_1)
:link(howto_2,Section_howto.html#howto_2)
:link(howto_3,Section_howto.html#howto_3)
:link(howto_4,Section_howto.html#howto_4)
:link(howto_5,Section_howto.html#howto_5)
:link(howto_6,Section_howto.html#howto_6)
:link(howto_7,Section_howto.html#howto_7)
:link(howto_8,Section_howto.html#howto_8)
:link(howto_9,Section_howto.html#howto_9)
:link(howto_10,Section_howto.html#howto_10)
:link(howto_11,Section_howto.html#howto_11)
:link(howto_12,Section_howto.html#howto_12)
:link(howto_13,Section_howto.html#howto_13)
:link(howto_14,Section_howto.html#howto_14)
:link(howto_15,Section_howto.html#howto_15)
:link(howto_16,Section_howto.html#howto_16)
:link(howto_17,Section_howto.html#howto_17)
:link(howto_18,Section_howto.html#howto_18)
:link(howto_19,Section_howto.html#howto_19)
:link(howto_20,Section_howto.html#howto_20)
:link(howto_21,Section_howto.html#howto_21)
:link(10_1,Section_howto.html#4_1)
:link(10_2,Section_howto.html#4_2)
:link(10_3,Section_howto.html#4_3)
:link(10_4,Section_howto.html#4_4)
:link(10_5,Section_howto.html#4_5)
:link(10_6,Section_howto.html#4_6)
:link(10_7,Section_howto.html#4_7)
:link(10_8,Section_howto.html#4_8)
:link(10_9,Section_howto.html#4_9)
:link(10_10,Section_howto.html#10_10)
:link(10_11,Section_howto.html#10_11)
:link(10_12,Section_howto.html#4_12)
:link(10_13,Section_howto.html#4_13)
:link(10_14,Section_howto.html#4_14)
:link(mod_1,Section_modify.html#mod_1)
:link(mod_2,Section_modify.html#mod_2)
:link(mod_3,Section_modify.html#mod_3)
:link(mod_4,Section_modify.html#mod_4)
:link(mod_5,Section_modify.html#mod_5)
:link(mod_6,Section_modify.html#mod_6)
:link(mod_7,Section_modify.html#mod_7)
:link(mod_8,Section_modify.html#mod_8)
:link(mod_9,Section_modify.html#mod_9)
:link(mod_10,Section_modify.html#mod_10)
:link(mod_11,Section_modify.html#mod_11)
:link(mod_12,Section_modify.html#mod_12)
:link(mod_13,Section_modify.html#mod_13)
:link(mod_14,Section_modify.html#mod_14)
:link(11_1,Section_python.html#9_1)
:link(11_2,Section_python.html#9_2)
:link(11_3,Section_python.html#9_3)
:link(11_4,Section_python.html#9_4)
:link(11_5,Section_python.html#9_5)
:link(11_6,Section_python.html#9_6)
:link(11_7,Section_python.html#9_7)
:link(py_1,Section_python.html#py_1)
: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)
</BODY>

30
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@ -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
@ -164,10 +164,10 @@ 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 +201,7 @@ 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>.
@ -306,10 +306,10 @@ 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 +363,16 @@ 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

26
doc/Section_accelerate.txt
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@ -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
@ -159,9 +159,9 @@ 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 +195,7 @@ 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
@ -300,9 +300,9 @@ 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 +356,16 @@ 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

21
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View File

@ -350,7 +350,8 @@ of each style or click on the style itself for a full description:
</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>
@ -386,7 +387,8 @@ 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>
@ -428,7 +430,8 @@ potentials. Click on the style itself for a full description:
</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>
@ -470,7 +473,8 @@ 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>
@ -490,7 +494,8 @@ 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>
@ -510,7 +515,8 @@ 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>
@ -541,7 +547,8 @@ 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>

21
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@ -481,7 +481,8 @@ 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.
"atc"_fix_atc.html,
"imd"_fix_imd.html,
@ -571,7 +572,8 @@ 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,
@ -660,7 +662,8 @@ potentials. Click on the style itself for a full description:
"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,
@ -747,7 +750,8 @@ 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)
@ -771,7 +775,8 @@ 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,
@ -795,7 +800,8 @@ 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)
@ -827,7 +833,8 @@ 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)

2
doc/Section_errors.html
View File

@ -152,7 +152,7 @@ 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.
</P>
<P>Also note that error messages from <A HREF = "Section_start.html#2_3">user-contributed
<P>Also note that error messages from <A HREF = "Section_start.html#start_3">user-contributed
packages</A> are not listed here. Is 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_errors.txt
View File

@ -150,7 +150,7 @@ not a bad idea! Note that sometimes the same message can be printed
from multiple places in the code.
Also note that error messages from "user-contributed
packages"_Section_start.html#2_3 are not listed here. Is such an
packages"_Section_start.html#start_3 are not listed here. Is 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.

39
doc/Section_howto.html
View File

@ -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
@ -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
@ -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
@ -1657,10 +1657,10 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
<A NAME = "6_19"></A><H4>6.19 Library interface to LAMMPS
</H4>
<P>As described in <A HREF = "Section_start.html#2_4">this section</A>, LAMMPS can be
built as a library, so that it can be called by another code, used in
a <A HREF = "Section_howto.html#6_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#6_10">coupled manner</A> with other codes, or
driven through a <A HREF = "Section_python.html">Python interface</A>.
</P>
<P>All of these methodologies use a C-style interface to LAMMPS that is
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

39
doc/Section_howto.txt
View File

@ -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
@ -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
@ -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
@ -1645,10 +1645,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
6.19 Library interface to LAMMPS :link(6_19),h4
As described in "this section"_Section_start.html#2_4, LAMMPS can be
built as a library, so that it can be called by another code, used in
a "coupled manner"_Section_howto.html#6_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#6_10 with other codes, or
driven through a "Python interface"_Section_python.html.
All of these methodologies use a C-style interface to LAMMPS that is
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

26
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
@ -254,7 +254,7 @@ 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
@ -372,7 +372,7 @@ 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-
@ -455,7 +455,7 @@ 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

26
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
@ -250,7 +250,7 @@ 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
@ -363,7 +363,7 @@ 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-
@ -445,7 +445,7 @@ 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

14
doc/Section_modify.html
View File

@ -538,13 +538,13 @@ then be accessed by variables) was discussed
<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

14
doc/Section_modify.txt
View File

@ -514,13 +514,13 @@ 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

19
doc/Section_python.html
View File

@ -23,13 +23,14 @@ 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
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#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.
</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
@ -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.
@ -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

19
doc/Section_python.txt
View File

@ -20,13 +20,14 @@ 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
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#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.
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
@ -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.
@ -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

105
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>
@ -350,7 +350,7 @@ 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 +369,7 @@ 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 +407,7 @@ 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 +462,18 @@ 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
@ -498,18 +498,18 @@ 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 LAMMPS 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
@ -563,7 +563,7 @@ 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
@ -625,7 +625,7 @@ 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 LAMMPS 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
@ -679,7 +679,7 @@ 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
@ -722,7 +722,7 @@ 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 +832,7 @@ 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 +861,13 @@ 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>
@ -983,9 +983,10 @@ partition screen files file.N.
</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.
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
"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
@ -1021,7 +1022,7 @@ input scripts.
</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 +1119,7 @@ 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

105
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]
@ -346,7 +346,7 @@ 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 +364,7 @@ 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 +402,7 @@ 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 +457,18 @@ 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
@ -493,18 +493,18 @@ 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 LAMMPS 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
@ -556,7 +556,7 @@ 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
@ -618,7 +618,7 @@ 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 LAMMPS 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
@ -672,7 +672,7 @@ 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
@ -715,7 +715,7 @@ 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 +822,7 @@ 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 +851,13 @@ 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
@ -973,9 +973,10 @@ partition screen files file.N.
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.
LAMMPS can be built with, as described above in "Section
2.3"_#start_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.
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/opt or
@ -1011,7 +1012,7 @@ input scripts.
: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 +1109,7 @@ 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/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>

2
doc/angle_charmm.txt
View File

@ -47,7 +47,7 @@ internally; hence the units of K are in energy/radian^2.
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_class2.html
View File

@ -81,7 +81,7 @@ same value from the Ea formula.
<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>
"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>

2
doc/angle_class2.txt
View File

@ -78,7 +78,7 @@ 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
"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_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>

2
doc/angle_cosine.txt
View File

@ -36,7 +36,7 @@ K (energy) :ul
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.
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>

2
doc/angle_cosine_delta.txt
View File

@ -41,7 +41,7 @@ internally.
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_cosine_periodic.html
View File

@ -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>

2
doc/angle_cosine_periodic.txt
View File

@ -49,7 +49,7 @@ geometry.
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

4
doc/angle_cosine_shift.html
View File

@ -41,8 +41,8 @@ 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>
section for more info on packages.
"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>
</P>

4
doc/angle_cosine_shift.txt
View File

@ -38,8 +38,8 @@ 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
section for more info on packages.
"user-misc" package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

4
doc/angle_cosine_shift_exp.html
View File

@ -53,8 +53,8 @@ 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>
section for more info on packages.
"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>
</P>

4
doc/angle_cosine_shift_exp.txt
View File

@ -50,8 +50,8 @@ 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
section for more info on packages.
"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>

2
doc/angle_cosine_squared.txt
View File

@ -41,7 +41,7 @@ internally.
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.
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>

2
doc/angle_harmonic.txt
View File

@ -41,7 +41,7 @@ internally; hence the units of K are in energy/radian^2.
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/angle_hybrid.html
View File

@ -77,7 +77,7 @@ for specific angle types.
<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

2
doc/angle_hybrid.txt
View File

@ -75,7 +75,7 @@ for specific angle types.
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.
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

6
doc/angle_style.html
View File

@ -84,9 +84,9 @@ page</A>.
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
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>

4
doc/angle_style.txt
View File

@ -83,8 +83,8 @@ defined.
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>

2
doc/angle_table.txt
View File

@ -122,7 +122,7 @@ one that matches the specified keyword.
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/atom_style.html
View File

@ -131,7 +131,7 @@ package. The <I>ellipsoid</I> style is part of the "asphere" package. The
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>
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>

2
doc/atom_style.txt
View File

@ -127,7 +127,7 @@ package. The {ellipsoid} style is part of the "asphere" package. The
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
with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
[Related commands:]

4
doc/bond_class2.html
View File

@ -43,8 +43,8 @@ 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 "class2"
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><B>Related commands:</B>
</P>

4
doc/bond_class2.txt
View File

@ -40,8 +40,8 @@ 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.
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]

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>

2
doc/bond_fene.txt
View File

@ -43,7 +43,7 @@ sigma (distance) :ul
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.
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>

2
doc/bond_fene_expand.txt
View File

@ -48,7 +48,7 @@ delta (distance) :ul
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.
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>

2
doc/bond_harmonic.txt
View File

@ -38,7 +38,7 @@ r0 (distance) :ul
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

4
doc/bond_harmonic_shift.html
View File

@ -45,8 +45,8 @@ 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>
section for more info on packages.
"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>
</P>

4
doc/bond_harmonic_shift.txt
View File

@ -40,8 +40,8 @@ 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
section for more info on packages.
"user-misc" package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

4
doc/bond_harmonic_shift_cut.html
View File

@ -43,8 +43,8 @@ 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>
section for more info on packages.
"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>
</P>

4
doc/bond_harmonic_shift_cut.txt
View File

@ -40,8 +40,8 @@ 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
section for more info on packages.
"user-misc" package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/bond_hybrid.html
View File

@ -60,7 +60,7 @@ bond types.
<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

2
doc/bond_hybrid.txt
View File

@ -58,7 +58,7 @@ bond types.
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.
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>

2
doc/bond_morse.txt
View File

@ -39,7 +39,7 @@ r0 (distance) :ul
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.
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>

2
doc/bond_nonlinear.txt
View File

@ -39,7 +39,7 @@ lamda (distance) :ul
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.
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>

2
doc/bond_quartic.txt
View File

@ -74,7 +74,7 @@ delete_bonds all bond 0 remove :pre
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.
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,

6
doc/bond_style.html
View File

@ -93,9 +93,9 @@ page</A>.
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
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>

4
doc/bond_style.txt
View File

@ -91,8 +91,8 @@ defined.
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>

2
doc/bond_table.txt
View File

@ -119,7 +119,7 @@ one that matches the specified keyword.
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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

2
doc/compute_ackland_atom.html
View File

@ -59,7 +59,7 @@ LAMMPS output options.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-misc" package. It is only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_ackland_atom.txt
View File

@ -57,7 +57,7 @@ LAMMPS output options.
This compute is part of the "user-misc" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

2
doc/compute_damage_atom.html
View File

@ -46,7 +46,7 @@ above.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "peri" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_damage_atom.txt
View File

@ -44,7 +44,7 @@ above.
This compute is part of the "peri" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

4
doc/compute_event_displace.html
View File

@ -55,8 +55,8 @@ scalar value will be a 0 or 1 as explained above.
<P><B>Restrictions:</B>
</P>
<P>This 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><B>Related commands:</B>
</P>

4
doc/compute_event_displace.txt
View File

@ -52,8 +52,8 @@ scalar value will be a 0 or 1 as explained above.
[Restrictions:]
This 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.
[Related commands:]

2
doc/compute_ke_atom_eff.html
View File

@ -70,7 +70,7 @@ output options.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_ke_atom_eff.txt
View File

@ -68,7 +68,7 @@ The per-atom vector values will be in energy "units"_units.html.
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

2
doc/compute_ke_eff.html
View File

@ -73,7 +73,7 @@ scalar value will be in energy <A HREF = "units.html">units</A>.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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> none

2
doc/compute_ke_eff.txt
View File

@ -71,7 +71,7 @@ scalar value will be in energy "units"_units.html.
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:] none

8
doc/compute_pe.html
View File

@ -67,12 +67,12 @@ except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the "user-cuda" 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.
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.

6
doc/compute_pe.txt
View File

@ -63,12 +63,12 @@ except for round-off and precision issues.
These accelerated styles are part of the "user-cuda" 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.
"Making LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.

8
doc/compute_pressure.html
View File

@ -97,12 +97,12 @@ except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the "user-cuda" 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.
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.

6
doc/compute_pressure.txt
View File

@ -93,12 +93,12 @@ except for round-off and precision issues.
These accelerated styles are part of the "user-cuda" 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.
"Making LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.

8
doc/compute_temp.html
View File

@ -77,12 +77,12 @@ except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the "user-cuda" 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.
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.

6
doc/compute_temp.txt
View File

@ -73,12 +73,12 @@ except for round-off and precision issues.
These accelerated styles are part of the "user-cuda" 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.
"Making LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.

2
doc/compute_temp_asphere.html
View File

@ -138,7 +138,7 @@ vector values will be in energy <A HREF = "units.html">units</A>.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This compute requires that atoms store angular momementum and a

2
doc/compute_temp_asphere.txt
View File

@ -131,7 +131,7 @@ vector values will be in energy "units"_units.html.
This compute is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
This compute requires that atoms store angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html

2
doc/compute_temp_deform_eff.html
View File

@ -64,7 +64,7 @@ vector values will be in energy <A HREF = "units.html">units</A>.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_temp_deform_eff.txt
View File

@ -62,7 +62,7 @@ vector values will be in energy "units"_units.html.
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

2
doc/compute_temp_eff.html
View File

@ -86,7 +86,7 @@ the simulation.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_temp_eff.txt
View File

@ -84,7 +84,7 @@ the simulation.
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

8
doc/compute_temp_partial.html
View File

@ -85,12 +85,12 @@ except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the "user-cuda" 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.
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.

6
doc/compute_temp_partial.txt
View File

@ -81,12 +81,12 @@ except for round-off and precision issues.
These accelerated styles are part of the "user-cuda" 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.
"Making LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.

2
doc/compute_temp_region_eff.html
View File

@ -55,7 +55,7 @@ vector values will be in energy <A HREF = "units.html">units</A>.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_temp_region_eff.txt
View File

@ -53,7 +53,7 @@ vector values will be in energy "units"_units.html.
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

2
doc/compute_temp_rotate.html
View File

@ -89,7 +89,7 @@ vector values will be in energy <A HREF = "units.html">units</A>.
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-misc" package. It is only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>

2
doc/compute_temp_rotate.txt
View File

@ -87,7 +87,7 @@ vector values will be in energy "units"_units.html.
This compute is part of the "user-misc" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

2
doc/dihedral_charmm.html
View File

@ -70,7 +70,7 @@ need any 1-4 information.
<P><B>Restrictions:</B>
</P>
<P>This dihedral 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>

2
doc/dihedral_charmm.txt
View File

@ -68,7 +68,7 @@ need any 1-4 information.
This dihedral 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.
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]

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