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patch to add DPD-VV

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This commit is contained in:
Steve Plimpton
2016-10-12 07:35:47 -06:00
parent 4a5d9eaae2
commit 63e71cd45b
6 changed files with 117 additions and 52 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <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="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."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
11 Oct 2016 version :c,h4 12 Oct 2016 version :c,h4
Version info: :h4 Version info: :h4

151
doc/src/Section_commands.txt
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@ -282,78 +282,135 @@ the "minimize"_minimize.html command. A parallel tempering
3.4 Commands listed by category :link(cmd_4),h4 3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_5 lists the same commands alphabetically. Note "next section"_#cmd_5 lists the same commands alphabetically. The
that some style options for some commands are part of specific LAMMPS next section also includes (long) lists of style options for entries
packages, which means they cannot be used unless the package was that appear in the following categories as a single command (fix,
included when LAMMPS was built. Not all packages are included in a compute, pair, etc). Commands that are added by user packages are not
default LAMMPS build. These dependencies are listed as Restrictions included in these categories, but they are in the next section.
in the command's documentation.
Initialization: Initialization:
"atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "newton"_newton.html,
"boundary"_boundary.html, "dimension"_dimension.html, "package"_package.html,
"newton"_newton.html, "processors"_processors.html, "units"_units.html "processors"_processors.html,
"suffix"_suffix.html,
"units"_units.html
Atom definition: Setup simulation box:
"create_atoms"_create_atoms.html, "create_box"_create_box.html, "boundary"_boundary.html,
"lattice"_lattice.html, "read_data"_read_data.html, "box"_box.html,
"read_dump"_read_dump.html, "read_restart"_read_restart.html, "change_box"_change_box.html,
"region"_region.html, "replicate"_replicate.html "create_box"_create_box.html,
"dimension"_dimension.html,
"lattice"_lattice.html,
"region"_region.html
Setup atoms:
"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: Force fields:
"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "angle_style"_angle_style.html,
"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.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, "dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html, "improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html, "improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "kspace_modify"_kspace_modify.html,
"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "kspace_style"_kspace_style.html,
"pair_style"_pair_style.html, "pair_write"_pair_write.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 "special_bonds"_special_bonds.html
Settings: Settings:
"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html, "comm_modify"_comm_modify.html,
"min_modify"_min_modify.html, "min_style"_min_style.html, "comm_style"_comm_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "info"_info.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "min_modify"_min_modify.html,
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.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
Fixes: Operations within timestepping (fixes) and diagnositics (computes):
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html "compute"_compute.html,
"compute_modify"_compute_modify.html,
Computes: "fix"_fix.html,
"fix_modify"_fix_modify.html,
"compute"_compute.html, "compute_modify"_compute_modify.html, "uncompute"_uncompute.html,
"uncompute"_uncompute.html "unfix"_unfix.html
Output: Output:
"dump"_dump.html, "dump image"_dump_image.html, "dump image"_dump_image.html,
"dump_modify"_dump_modify.html, "dump movie"_dump_image.html, "dump movie"_dump_image.html,
"restart"_restart.html, "thermo"_thermo.html, "dump"_dump.html,
"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "dump_modify"_dump_modify.html,
"undump"_undump.html, "write_data"_write_data.html, "restart"_restart.html,
"write_dump"_write_dump.html, "write_restart"_write_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: Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "minimize"_minimize.html,
"displace_atoms"_displace_atoms.html, "change_box"_change_box.html, "neb"_neb.html,
"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html, "prd"_prd.html,
"rerun"_rerun.html, "run"_run.html, "temper"_temper.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, "clear"_clear.html,
"include"_include.html, "jump"_jump.html, "label"_label.html, "echo"_echo.html,
"log"_log.html, "next"_next.html, "print"_print.html, "if"_if.html,
"shell"_shell.html, "variable"_variable.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 :line

4
doc/src/fix_temp_berendsen.txt
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@ -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 name. In this case, the variable will be evaluated each timestep, and
its value used to determine the target temperature. 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 Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed keywords for the simulation box parameters and timestep and elapsed

6
doc/src/fix_temp_rescale.txt
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@ -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 ramped value between the {Tstart} and {Tstop} temperatures at the
beginning and end of the run. 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. {Tstart} can be specified as an equal-style "variable"_variable.html.
In this case, the {Tstop} setting is ignored. If the value is a 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 variable, it should be specified as v_name, where name is the variable
@ -50,7 +54,7 @@ name. In this case, the variable will be evaluated each timestep, and
its value used to determine the target temperature. its value used to determine the target temperature.
Equal-style variables can specify formulas with various mathematical 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 keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature. time. Thus it is easy to specify a time-dependent temperature.

2
src/fix_temp_rescale.cpp
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@ -139,7 +139,7 @@ void FixTempRescale::end_of_step()
if (temperature->dof < 1) return; if (temperature->dof < 1) return;
// protect against division by zero. // protect against division by zero
if (t_current == 0.0) if (t_current == 0.0)
error->all(FLERR,"Computed temperature for fix temp/rescale cannot be 0.0"); error->all(FLERR,"Computed temperature for fix temp/rescale cannot be 0.0");

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "11 Oct 2016" #define LAMMPS_VERSION "12 Oct 2016"