Loading doc/Makefile +8 −4 Original line number Diff line number Diff line Loading @@ -8,13 +8,15 @@ VENV = $(BUILDDIR)/docenv TXT2RST = $(VENV)/bin/txt2rst PYTHON = $(shell which python3) HAS_PYTHON3 = NO HAS_VIRTUALENV = NO ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1) $(error Python3 was not found! Please check README.md for further instructions) ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0) HAS_PYTHON3 = YES endif ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1) $(error virtualenv was not found! Please check README.md for further instructions) ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0) HAS_VIRTUALENV = YES endif SOURCES=$(wildcard src/*.txt) Loading Loading @@ -109,6 +111,8 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST) ) $(VENV): @if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @( \ virtualenv -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ Loading doc/README +0 −3 Original line number Diff line number Diff line Loading @@ -91,6 +91,3 @@ This will install virtualenv from the Python Package Index. ---------------- Installing prerequisites for PDF build doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="11 Oct 2016 version"> <META NAME="docnumber" CONTENT="18 Oct 2016 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 11 Oct 2016 version :c,h4 18 Oct 2016 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +106 −48 Original line number Diff line number Diff line Loading @@ -282,78 +282,135 @@ the "minimize"_minimize.html command. A parallel tempering 3.4 Commands listed by category :link(cmd_4),h4 This section lists all LAMMPS commands, grouped by category. The "next section"_#cmd_5 lists the same commands alphabetically. Note that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions in the command's documentation. "next section"_#cmd_5 lists the same commands alphabetically. The next section also includes (long) lists of style options for entries that appear in the following categories as a single command (fix, compute, pair, etc). Commands that are added by user packages are not included in these categories, but they are in the next section. Initialization: "atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "boundary"_boundary.html, "dimension"_dimension.html, "newton"_newton.html, "processors"_processors.html, "units"_units.html "newton"_newton.html, "package"_package.html, "processors"_processors.html, "suffix"_suffix.html, "units"_units.html Setup simulation box: "boundary"_boundary.html, "box"_box.html, "change_box"_change_box.html, "create_box"_create_box.html, "dimension"_dimension.html, "lattice"_lattice.html, "region"_region.html Atom definition: Setup atoms: "create_atoms"_create_atoms.html, "create_box"_create_box.html, "lattice"_lattice.html, "read_data"_read_data.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html, "region"_region.html, "replicate"_replicate.html "atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "balance"_balance.html, "create_atoms"_create_atoms.html, "create_bonds"_create_bonds.html, "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "displace_atoms"_displace_atoms.html, "group"_group.html, "mass"_mass.html, "molecule"_molecule.html, "read_data"_read_data.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html, "replicate"_replicate.html, "set"_set.html, "velocity"_velocity.html Force fields: "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html, "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "bond_write"_bond_write.html, "dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html, "dihedral_style"_dihedral_style.html, "improper_coeff"_improper_coeff.html, "improper_style"_improper_style.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "pair_style"_pair_style.html, "pair_write"_pair_write.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "pair_style"_pair_style.html, "pair_write"_pair_write.html, "special_bonds"_special_bonds.html Settings: "comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html Fixes: "fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html "comm_modify"_comm_modify.html, "comm_style"_comm_style.html, "info"_info.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "partition"_partition.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "timer"_timer.html, "timestep"_timestep.html Computes: Operations within timestepping (fixes) and diagnositics (computes): "compute"_compute.html, "compute_modify"_compute_modify.html, "uncompute"_uncompute.html "compute"_compute.html, "compute_modify"_compute_modify.html, "fix"_fix.html, "fix_modify"_fix_modify.html, "uncompute"_uncompute.html, "unfix"_unfix.html Output: "dump"_dump.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html, "dump movie"_dump_image.html, "restart"_restart.html, "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "undump"_undump.html, "write_data"_write_data.html, "write_dump"_write_dump.html, "write_restart"_write_restart.html "dump image"_dump_image.html, "dump movie"_dump_image.html, "dump"_dump.html, "dump_modify"_dump_modify.html, "restart"_restart.html, "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "undump"_undump.html, "write_coeff"_write_coeff.html, "write_data"_write_data.html, "write_dump"_write_dump.html, "write_restart"_write_restart.html Actions: "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "displace_atoms"_displace_atoms.html, "change_box"_change_box.html, "minimize"_minimize.html, "neb"_neb.html "prd"_prd.html, "rerun"_rerun.html, "run"_run.html, "temper"_temper.html "minimize"_minimize.html, "neb"_neb.html, "prd"_prd.html, "rerun"_rerun.html, "run"_run.html, "tad"_tad.html, "temper"_temper.html Miscellaneous: Input script control: "clear"_clear.html, "echo"_echo.html, "if"_if.html, "include"_include.html, "jump"_jump.html, "label"_label.html, "log"_log.html, "next"_next.html, "print"_print.html, "shell"_shell.html, "variable"_variable.html "clear"_clear.html, "echo"_echo.html, "if"_if.html, "include"_include.html, "jump"_jump.html, "label"_label.html, "log"_log.html, "next"_next.html, "print"_print.html, "python"_python.html, "quit"_quit.html, "shell"_shell.html, "variable"_variable.html :line Loading Loading @@ -516,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "gcmc"_fix_gcmc.html, "gld"_fix_gld.html, "gravity (o)"_fix_gravity.html, "halt"_fix_halt.html, "heat"_fix_heat.html, "indent"_fix_indent.html, "langevin (k)"_fix_langevin.html, Loading Loading @@ -924,7 +982,7 @@ KOKKOS, o = USER-OMP, t = OPT. "tip4p/long (o)"_pair_coul.html, "tri/lj"_pair_tri_lj.html, "vashishta (o)"_pair_vashishta.html, "vashishta/table (o)"_pair_vashishta_table.html, "vashishta/table (o)"_pair_vashishta.html, "yukawa (go)"_pair_yukawa.html, "yukawa/colloid (go)"_pair_yukawa_colloid.html, "zbl (go)"_pair_zbl.html :tb(c=4,ea=c) Loading doc/src/compute_pe_atom.txt +4 −3 Original line number Diff line number Diff line Loading @@ -72,9 +72,10 @@ compute peratom all pe/atom compute pe all reduce sum c_peratom thermo_style custom step temp etotal press pe c_pe :pre NOTE: The per-atom energy does not any Lennard-Jones tail corrections invoked by the "pair_modify tail yes"_pair_modify.html command, since those are global contributions to the system energy. NOTE: The per-atom energy does not include any Lennard-Jones tail corrections to the energy added by the "pair_modify tail yes"_pair_modify.html command, since those are contributions to the global system energy. [Output info:] Loading Loading
doc/Makefile +8 −4 Original line number Diff line number Diff line Loading @@ -8,13 +8,15 @@ VENV = $(BUILDDIR)/docenv TXT2RST = $(VENV)/bin/txt2rst PYTHON = $(shell which python3) HAS_PYTHON3 = NO HAS_VIRTUALENV = NO ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1) $(error Python3 was not found! Please check README.md for further instructions) ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0) HAS_PYTHON3 = YES endif ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1) $(error virtualenv was not found! Please check README.md for further instructions) ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0) HAS_VIRTUALENV = YES endif SOURCES=$(wildcard src/*.txt) Loading Loading @@ -109,6 +111,8 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST) ) $(VENV): @if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @( \ virtualenv -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ Loading
doc/README +0 −3 Original line number Diff line number Diff line Loading @@ -91,6 +91,3 @@ This will install virtualenv from the Python Package Index. ---------------- Installing prerequisites for PDF build
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="11 Oct 2016 version"> <META NAME="docnumber" CONTENT="18 Oct 2016 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 11 Oct 2016 version :c,h4 18 Oct 2016 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +106 −48 Original line number Diff line number Diff line Loading @@ -282,78 +282,135 @@ the "minimize"_minimize.html command. A parallel tempering 3.4 Commands listed by category :link(cmd_4),h4 This section lists all LAMMPS commands, grouped by category. The "next section"_#cmd_5 lists the same commands alphabetically. Note that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions in the command's documentation. "next section"_#cmd_5 lists the same commands alphabetically. The next section also includes (long) lists of style options for entries that appear in the following categories as a single command (fix, compute, pair, etc). Commands that are added by user packages are not included in these categories, but they are in the next section. Initialization: "atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "boundary"_boundary.html, "dimension"_dimension.html, "newton"_newton.html, "processors"_processors.html, "units"_units.html "newton"_newton.html, "package"_package.html, "processors"_processors.html, "suffix"_suffix.html, "units"_units.html Setup simulation box: "boundary"_boundary.html, "box"_box.html, "change_box"_change_box.html, "create_box"_create_box.html, "dimension"_dimension.html, "lattice"_lattice.html, "region"_region.html Atom definition: Setup atoms: "create_atoms"_create_atoms.html, "create_box"_create_box.html, "lattice"_lattice.html, "read_data"_read_data.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html, "region"_region.html, "replicate"_replicate.html "atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "balance"_balance.html, "create_atoms"_create_atoms.html, "create_bonds"_create_bonds.html, "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "displace_atoms"_displace_atoms.html, "group"_group.html, "mass"_mass.html, "molecule"_molecule.html, "read_data"_read_data.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html, "replicate"_replicate.html, "set"_set.html, "velocity"_velocity.html Force fields: "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html, "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "bond_write"_bond_write.html, "dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html, "dihedral_style"_dihedral_style.html, "improper_coeff"_improper_coeff.html, "improper_style"_improper_style.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "pair_style"_pair_style.html, "pair_write"_pair_write.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "pair_style"_pair_style.html, "pair_write"_pair_write.html, "special_bonds"_special_bonds.html Settings: "comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html Fixes: "fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html "comm_modify"_comm_modify.html, "comm_style"_comm_style.html, "info"_info.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "partition"_partition.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "timer"_timer.html, "timestep"_timestep.html Computes: Operations within timestepping (fixes) and diagnositics (computes): "compute"_compute.html, "compute_modify"_compute_modify.html, "uncompute"_uncompute.html "compute"_compute.html, "compute_modify"_compute_modify.html, "fix"_fix.html, "fix_modify"_fix_modify.html, "uncompute"_uncompute.html, "unfix"_unfix.html Output: "dump"_dump.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html, "dump movie"_dump_image.html, "restart"_restart.html, "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "undump"_undump.html, "write_data"_write_data.html, "write_dump"_write_dump.html, "write_restart"_write_restart.html "dump image"_dump_image.html, "dump movie"_dump_image.html, "dump"_dump.html, "dump_modify"_dump_modify.html, "restart"_restart.html, "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "undump"_undump.html, "write_coeff"_write_coeff.html, "write_data"_write_data.html, "write_dump"_write_dump.html, "write_restart"_write_restart.html Actions: "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "displace_atoms"_displace_atoms.html, "change_box"_change_box.html, "minimize"_minimize.html, "neb"_neb.html "prd"_prd.html, "rerun"_rerun.html, "run"_run.html, "temper"_temper.html "minimize"_minimize.html, "neb"_neb.html, "prd"_prd.html, "rerun"_rerun.html, "run"_run.html, "tad"_tad.html, "temper"_temper.html Miscellaneous: Input script control: "clear"_clear.html, "echo"_echo.html, "if"_if.html, "include"_include.html, "jump"_jump.html, "label"_label.html, "log"_log.html, "next"_next.html, "print"_print.html, "shell"_shell.html, "variable"_variable.html "clear"_clear.html, "echo"_echo.html, "if"_if.html, "include"_include.html, "jump"_jump.html, "label"_label.html, "log"_log.html, "next"_next.html, "print"_print.html, "python"_python.html, "quit"_quit.html, "shell"_shell.html, "variable"_variable.html :line Loading Loading @@ -516,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "gcmc"_fix_gcmc.html, "gld"_fix_gld.html, "gravity (o)"_fix_gravity.html, "halt"_fix_halt.html, "heat"_fix_heat.html, "indent"_fix_indent.html, "langevin (k)"_fix_langevin.html, Loading Loading @@ -924,7 +982,7 @@ KOKKOS, o = USER-OMP, t = OPT. "tip4p/long (o)"_pair_coul.html, "tri/lj"_pair_tri_lj.html, "vashishta (o)"_pair_vashishta.html, "vashishta/table (o)"_pair_vashishta_table.html, "vashishta/table (o)"_pair_vashishta.html, "yukawa (go)"_pair_yukawa.html, "yukawa/colloid (go)"_pair_yukawa_colloid.html, "zbl (go)"_pair_zbl.html :tb(c=4,ea=c) Loading
doc/src/compute_pe_atom.txt +4 −3 Original line number Diff line number Diff line Loading @@ -72,9 +72,10 @@ compute peratom all pe/atom compute pe all reduce sum c_peratom thermo_style custom step temp etotal press pe c_pe :pre NOTE: The per-atom energy does not any Lennard-Jones tail corrections invoked by the "pair_modify tail yes"_pair_modify.html command, since those are global contributions to the system energy. NOTE: The per-atom energy does not include any Lennard-Jones tail corrections to the energy added by the "pair_modify tail yes"_pair_modify.html command, since those are contributions to the global system energy. [Output info:] Loading
