Loading 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="12 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 12 Oct 2016 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +104 −47 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 doc/src/fix_temp_berendsen.txt +4 −0 Original line number Diff line number Diff line Loading @@ -49,6 +49,10 @@ variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. NOTE: This thermostat will generate an error if the current temperature is zero at the end of a timestep. It cannot rescale a zero temperature. Equal-style variables can specify formulas with various mathematical functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed Loading doc/src/fix_temp_rescale.txt +5 −1 Original line number Diff line number Diff line Loading @@ -43,6 +43,10 @@ Rescaling is performed every N timesteps. The target temperature is a ramped value between the {Tstart} and {Tstop} temperatures at the beginning and end of the run. NOTE: This thermostat will generate an error if the current temperature is zero at the end of a timestep it is inovoked on. It cannot rescale a zero temperature. {Tstart} can be specified as an equal-style "variable"_variable.html. In this case, the {Tstop} setting is ignored. If the value is a variable, it should be specified as v_name, where name is the variable Loading @@ -50,7 +54,7 @@ name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical functions, and include "thermo_style"_thermo_style.html command functions, and include "thermo_style"_thermox_style.html command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. Loading src/fix_temp_rescale.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -139,7 +139,7 @@ void FixTempRescale::end_of_step() if (temperature->dof < 1) return; // protect against division by zero. // protect against division by zero if (t_current == 0.0) error->all(FLERR,"Computed temperature for fix temp/rescale cannot be 0.0"); Loading Loading
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="12 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 12 Oct 2016 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +104 −47 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
doc/src/fix_temp_berendsen.txt +4 −0 Original line number Diff line number Diff line Loading @@ -49,6 +49,10 @@ variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. NOTE: This thermostat will generate an error if the current temperature is zero at the end of a timestep. It cannot rescale a zero temperature. Equal-style variables can specify formulas with various mathematical functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed Loading
doc/src/fix_temp_rescale.txt +5 −1 Original line number Diff line number Diff line Loading @@ -43,6 +43,10 @@ Rescaling is performed every N timesteps. The target temperature is a ramped value between the {Tstart} and {Tstop} temperatures at the beginning and end of the run. NOTE: This thermostat will generate an error if the current temperature is zero at the end of a timestep it is inovoked on. It cannot rescale a zero temperature. {Tstart} can be specified as an equal-style "variable"_variable.html. In this case, the {Tstop} setting is ignored. If the value is a variable, it should be specified as v_name, where name is the variable Loading @@ -50,7 +54,7 @@ name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical functions, and include "thermo_style"_thermo_style.html command functions, and include "thermo_style"_thermox_style.html command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. Loading
src/fix_temp_rescale.cpp +1 −1 Original line number Diff line number Diff line Loading @@ -139,7 +139,7 @@ void FixTempRescale::end_of_step() if (temperature->dof < 1) return; // protect against division by zero. // protect against division by zero if (t_current == 0.0) error->all(FLERR,"Computed temperature for fix temp/rescale cannot be 0.0"); Loading
