Loading doc/src/Section_commands.txt +2 −0 Original line number Diff line number Diff line Loading @@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "press/berendsen"_fix_press_berendsen.html, "print"_fix_print.html, "property/atom"_fix_property_atom.html, "python"_fix_python.html, "qeq/comb (o)"_fix_qeq_comb.html, "qeq/dynamic"_fix_qeq.html, "qeq/fire"_fix_qeq.html, Loading Loading @@ -984,6 +985,7 @@ KOKKOS, o = USER-OMP, t = OPT. "peri/pmb (o)"_pair_peri.html, "peri/ves"_pair_peri.html, "polymorphic"_pair_polymorphic.html, "python"_pair_python.html, "reax"_pair_reax.html, "rebo (o)"_pair_airebo.html, "resquared (go)"_pair_resquared.html, Loading doc/src/Section_python.txt +26 −13 Original line number Diff line number Diff line Loading @@ -118,13 +118,21 @@ check which version of Python you have installed, by simply typing 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 LAMMPS has a "python"_python.html command which can be used in an input script to define and execute a Python function that you write the code for. The Python function can also be assigned to a LAMMPS python-style variable via the "variable"_variable.html command. Each time the variable is evaluated, either in the LAMMPS input script itself, or by another LAMMPS command that uses the variable, this will trigger the Python function to be invoked. LAMMPS has several commands which can be used to invoke Python code directly from an input script: "python"_python.html "variable python"_variable.html "fix python"_fix_python.html "pair_style python"_pair_python.html :ul The "python"_python.html command which can be used to define and execute a Python function that you write the code for. The Python function can also be assigned to a LAMMPS python-style variable via the "variable"_variable.html command. Each time the variable is evaluated, either in the LAMMPS input script itself, or by another LAMMPS command that uses the variable, this will trigger the Python function to be invoked. The Python code for the function can be included directly in the input script or in an auxiliary file. The function can have arguments which Loading Loading @@ -155,13 +163,18 @@ commands. See the "python"_python.html doc page and the "variable"_variable.html doc page for its python-style variables for more info, including examples of Python code you can write for both pure Python operations and callbacks to LAMMPS. See "fix python"_fix_python.html to learn about possibilities to execute Python code during each time step. Through the "python pair style"_pair_python.html it is also possible to define potential functions as python code. and callbacks to LAMMPS. To run pure Python code from LAMMPS, you only need to build LAMMPS with the PYTHON package installed: The "fix python"_fix_python.html command can execute Python code at selected timesteps during a simulation run. The "pair_style python"_pair_python command allows you to define pairwise potentials as python code which encodes a single pairwise interaction. This is useful for rapid-developement and debugging of a new potential. To use any of these commands, you only need to build LAMMPS with the PYTHON package installed: make yes-python make machine :pre Loading doc/src/fix_reax_bonds.txt +14 −1 Original line number Diff line number Diff line Loading @@ -34,7 +34,20 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. The format of the output file should be self-explanatory. The format of the output file should be reasonably self-explanatory. The meaning of the column header abbreviations is as follows: id = atom id type = atom type nb = number of bonds id_1 = atom id of first bond id_nb = atom id of Nth bond mol = molecule id bo_1 = bond order of first bond bo_nb = bond order of Nth bond abo = atom bond order (sum of all bonds) nlp = number of lone pairs q = atomic charge :ul If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text Loading doc/src/pair_edip.txt +5 −4 Original line number Diff line number Diff line Loading @@ -7,12 +7,13 @@ :line pair_style edip command :h3 pair_style edip/multi command :h3 [Syntax:] pair_style edip :pre pair_style edip/omp :pre pair_style edip/multi :pre pair_style style :pre style = {edip} or {edip/multi} :ul [Examples:] Loading Loading @@ -168,4 +169,4 @@ appropriate units if your simulation doesn't use "metal" units. :line :link(EDIP) [(EDIP)] J. F. Justo et al., Phys. Rev. B 58, 2539 (1998). [(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998). doc/src/pair_gw.txt +3 −1 Original line number Diff line number Diff line Loading @@ -11,7 +11,9 @@ pair_style gw/zbl command :h3 [Syntax:] pair_style gw :pre pair_style style :pre style = {gw} or {gw/zbl} :ul [Examples:] Loading Loading
doc/src/Section_commands.txt +2 −0 Original line number Diff line number Diff line Loading @@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "press/berendsen"_fix_press_berendsen.html, "print"_fix_print.html, "property/atom"_fix_property_atom.html, "python"_fix_python.html, "qeq/comb (o)"_fix_qeq_comb.html, "qeq/dynamic"_fix_qeq.html, "qeq/fire"_fix_qeq.html, Loading Loading @@ -984,6 +985,7 @@ KOKKOS, o = USER-OMP, t = OPT. "peri/pmb (o)"_pair_peri.html, "peri/ves"_pair_peri.html, "polymorphic"_pair_polymorphic.html, "python"_pair_python.html, "reax"_pair_reax.html, "rebo (o)"_pair_airebo.html, "resquared (go)"_pair_resquared.html, Loading
doc/src/Section_python.txt +26 −13 Original line number Diff line number Diff line Loading @@ -118,13 +118,21 @@ check which version of Python you have installed, by simply typing 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 LAMMPS has a "python"_python.html command which can be used in an input script to define and execute a Python function that you write the code for. The Python function can also be assigned to a LAMMPS python-style variable via the "variable"_variable.html command. Each time the variable is evaluated, either in the LAMMPS input script itself, or by another LAMMPS command that uses the variable, this will trigger the Python function to be invoked. LAMMPS has several commands which can be used to invoke Python code directly from an input script: "python"_python.html "variable python"_variable.html "fix python"_fix_python.html "pair_style python"_pair_python.html :ul The "python"_python.html command which can be used to define and execute a Python function that you write the code for. The Python function can also be assigned to a LAMMPS python-style variable via the "variable"_variable.html command. Each time the variable is evaluated, either in the LAMMPS input script itself, or by another LAMMPS command that uses the variable, this will trigger the Python function to be invoked. The Python code for the function can be included directly in the input script or in an auxiliary file. The function can have arguments which Loading Loading @@ -155,13 +163,18 @@ commands. See the "python"_python.html doc page and the "variable"_variable.html doc page for its python-style variables for more info, including examples of Python code you can write for both pure Python operations and callbacks to LAMMPS. See "fix python"_fix_python.html to learn about possibilities to execute Python code during each time step. Through the "python pair style"_pair_python.html it is also possible to define potential functions as python code. and callbacks to LAMMPS. To run pure Python code from LAMMPS, you only need to build LAMMPS with the PYTHON package installed: The "fix python"_fix_python.html command can execute Python code at selected timesteps during a simulation run. The "pair_style python"_pair_python command allows you to define pairwise potentials as python code which encodes a single pairwise interaction. This is useful for rapid-developement and debugging of a new potential. To use any of these commands, you only need to build LAMMPS with the PYTHON package installed: make yes-python make machine :pre Loading
doc/src/fix_reax_bonds.txt +14 −1 Original line number Diff line number Diff line Loading @@ -34,7 +34,20 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. The format of the output file should be self-explanatory. The format of the output file should be reasonably self-explanatory. The meaning of the column header abbreviations is as follows: id = atom id type = atom type nb = number of bonds id_1 = atom id of first bond id_nb = atom id of Nth bond mol = molecule id bo_1 = bond order of first bond bo_nb = bond order of Nth bond abo = atom bond order (sum of all bonds) nlp = number of lone pairs q = atomic charge :ul If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text Loading
doc/src/pair_edip.txt +5 −4 Original line number Diff line number Diff line Loading @@ -7,12 +7,13 @@ :line pair_style edip command :h3 pair_style edip/multi command :h3 [Syntax:] pair_style edip :pre pair_style edip/omp :pre pair_style edip/multi :pre pair_style style :pre style = {edip} or {edip/multi} :ul [Examples:] Loading Loading @@ -168,4 +169,4 @@ appropriate units if your simulation doesn't use "metal" units. :line :link(EDIP) [(EDIP)] J. F. Justo et al., Phys. Rev. B 58, 2539 (1998). [(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998).
doc/src/pair_gw.txt +3 −1 Original line number Diff line number Diff line Loading @@ -11,7 +11,9 @@ pair_style gw/zbl command :h3 [Syntax:] pair_style gw :pre pair_style style :pre style = {gw} or {gw/zbl} :ul [Examples:] Loading
