Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line Loading @@ -116,7 +116,7 @@ it gives quick access to documentation for all LAMMPS commands. Section_howto Section_example Section_perf Section_tools Tools Section_modify Section_python Section_errors Loading Loading @@ -210,7 +210,7 @@ END_RST --> 6.27 "Drude induced dipoles"_howto_27 :ule,b "Example problems"_Section_example.html :l "Performance & scalability"_Section_perf.html :l "Additional tools"_Section_tools.html :l "Auxiliary tools"_Tools.html :l "Modifying & extending LAMMPS"_Section_modify.html :l 10.1 "Atom styles"_mod_1 :ulb,b 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b Loading doc/src/Section_howto.txt +9 −9 Original line number Diff line number Diff line Loading @@ -188,9 +188,9 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the "read_data"_read_data.html command or in the input script with commands like "pair_coeff"_pair_coeff.html or "bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input. "bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input. See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force Loading Loading @@ -762,12 +762,12 @@ simulations can be visualized (and analyzed) in a variety of ways. LAMMPS snapshots are created by the "dump"_dump.html command which can create files in several formats. The native LAMMPS dump format is a text file (see "dump atom" or "dump custom") which can be visualized by several popular visualization tools. The "dump image"_dump_image.html and "dump movie"_dump_image.html styles can output internally rendered images and convert a sequence of them to a movie during the MD run. Several programs included with LAMMPS as auxiliary tools can convert between LAMMPS format files and other formats. See the "Section 9"_Section_tools.html doc page for details. by several popular visualization tools. The "dump image"_dump_image.html and "dump movie"_dump_image.html styles can output internally rendered images and convert a sequence of them to a movie during the MD run. Several programs included with LAMMPS as auxiliary tools can convert between LAMMPS format files and other formats. See the "Tools"_Tools.html doc page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of Loading doc/src/Section_intro.txt +9 −9 Original line number Diff line number Diff line Loading @@ -234,8 +234,8 @@ Multi-replica models :h4 Pre- and post-processing :h4 Various pre- and post-processing serial tools are packaged with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l Various pre- and post-processing serial tools are packaged with LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, Loading Loading @@ -296,9 +296,9 @@ visualize your MD simulation plot your output data :ul A few tools for pre- and post-processing tasks are provided as part of the LAMMPS package; they are described in "this section"_Section_tools.html. However, many people use other codes or write their own tools for these tasks. the LAMMPS package; they are described on the "Tools"_Tools.html doc page. However, many people use other codes or write their own tools for these tasks. As noted above, our group has also written and released a separate toolkit called "Pizza.py"_pizza which addresses some of the listed Loading Loading @@ -327,8 +327,8 @@ topology information and hundreds of force-field coefficients must typically be specified. We suggest you use a program like "CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup such problems and dump its information to a file. You can then reformat the file as LAMMPS input. Some of the tools in "this section"_Section_tools.html can assist in this process. reformat the file as LAMMPS input. Some of the tools described on the "Tools"_Tools.html doc page can assist in this process. Similarly, LAMMPS creates output files in a simple format. Most users post-process these files with their own analysis tools or re-format Loading Loading @@ -442,8 +442,8 @@ directory. :l The tools sub-directory of the LAMMPS distribution has various stand-alone codes for pre- and post-processing of LAMMPS data. More details are given in "Section 9"_Section_tools.html. If you write a new tool that users will find useful, it can be added to the LAMMPS details are given on the "Tools"_Tools.html doc page. If you write a new tool that users will find useful, it can be added to the LAMMPS distribution. :l LAMMPS is designed to be easy to extend with new code for features Loading doc/src/Section_modify.txt +2 −2 Original line number Diff line number Diff line "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next "Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_python.html :c :link(lws,http://lammps.sandia.gov) Loading doc/src/Section_perf.txt +3 −1 Original line number Diff line number Diff line "Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c "Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line Loading @@ -116,7 +116,7 @@ it gives quick access to documentation for all LAMMPS commands. Section_howto Section_example Section_perf Section_tools Tools Section_modify Section_python Section_errors Loading Loading @@ -210,7 +210,7 @@ END_RST --> 6.27 "Drude induced dipoles"_howto_27 :ule,b "Example problems"_Section_example.html :l "Performance & scalability"_Section_perf.html :l "Additional tools"_Section_tools.html :l "Auxiliary tools"_Tools.html :l "Modifying & extending LAMMPS"_Section_modify.html :l 10.1 "Atom styles"_mod_1 :ulb,b 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b Loading
doc/src/Section_howto.txt +9 −9 Original line number Diff line number Diff line Loading @@ -188,9 +188,9 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the "read_data"_read_data.html command or in the input script with commands like "pair_coeff"_pair_coeff.html or "bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input. "bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input. See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force Loading Loading @@ -762,12 +762,12 @@ simulations can be visualized (and analyzed) in a variety of ways. LAMMPS snapshots are created by the "dump"_dump.html command which can create files in several formats. The native LAMMPS dump format is a text file (see "dump atom" or "dump custom") which can be visualized by several popular visualization tools. The "dump image"_dump_image.html and "dump movie"_dump_image.html styles can output internally rendered images and convert a sequence of them to a movie during the MD run. Several programs included with LAMMPS as auxiliary tools can convert between LAMMPS format files and other formats. See the "Section 9"_Section_tools.html doc page for details. by several popular visualization tools. The "dump image"_dump_image.html and "dump movie"_dump_image.html styles can output internally rendered images and convert a sequence of them to a movie during the MD run. Several programs included with LAMMPS as auxiliary tools can convert between LAMMPS format files and other formats. See the "Tools"_Tools.html doc page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of Loading
doc/src/Section_intro.txt +9 −9 Original line number Diff line number Diff line Loading @@ -234,8 +234,8 @@ Multi-replica models :h4 Pre- and post-processing :h4 Various pre- and post-processing serial tools are packaged with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l Various pre- and post-processing serial tools are packaged with LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, Loading Loading @@ -296,9 +296,9 @@ visualize your MD simulation plot your output data :ul A few tools for pre- and post-processing tasks are provided as part of the LAMMPS package; they are described in "this section"_Section_tools.html. However, many people use other codes or write their own tools for these tasks. the LAMMPS package; they are described on the "Tools"_Tools.html doc page. However, many people use other codes or write their own tools for these tasks. As noted above, our group has also written and released a separate toolkit called "Pizza.py"_pizza which addresses some of the listed Loading Loading @@ -327,8 +327,8 @@ topology information and hundreds of force-field coefficients must typically be specified. We suggest you use a program like "CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup such problems and dump its information to a file. You can then reformat the file as LAMMPS input. Some of the tools in "this section"_Section_tools.html can assist in this process. reformat the file as LAMMPS input. Some of the tools described on the "Tools"_Tools.html doc page can assist in this process. Similarly, LAMMPS creates output files in a simple format. Most users post-process these files with their own analysis tools or re-format Loading Loading @@ -442,8 +442,8 @@ directory. :l The tools sub-directory of the LAMMPS distribution has various stand-alone codes for pre- and post-processing of LAMMPS data. More details are given in "Section 9"_Section_tools.html. If you write a new tool that users will find useful, it can be added to the LAMMPS details are given on the "Tools"_Tools.html doc page. If you write a new tool that users will find useful, it can be added to the LAMMPS distribution. :l LAMMPS is designed to be easy to extend with new code for features Loading
doc/src/Section_modify.txt +2 −2 Original line number Diff line number Diff line "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next "Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_python.html :c :link(lws,http://lammps.sandia.gov) Loading
doc/src/Section_perf.txt +3 −1 Original line number Diff line number Diff line "Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c "Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) Loading
