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merge set_time command into reset_timestep

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This commit is contained in:
Axel Kohlmeyer
2022-05-04 13:24:23 -04:00
parent 0bedff1ce0
commit f8742d599b
8 changed files with 65 additions and 108 deletions
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1
doc/src/Commands_all.rst
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@ -105,7 +105,6 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`run <run>`
* :doc:`run_style <run_style>`
* :doc:`set <set>`
* :doc:`set_time <set_time>`
* :doc:`shell <shell>`
* :doc:`special_bonds <special_bonds>`
* :doc:`suffix <suffix>`

1
doc/src/commands_list.rst
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@ -96,7 +96,6 @@ Commands
run
run_style
set
set_time
shell
special_bonds
suffix

59
doc/src/reset_timestep.rst
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@ -8,9 +8,16 @@ Syntax
.. code-block:: LAMMPS
reset_timestep N
reset_timestep N keyword values ...
* N = timestep number
* N = timestep number (may be NULL)
* zero or more keyword/value pairs may be appended
* keyword = *time*
.. parsed-literal::
*time* value = atime
atime = accumulated simulation time
Examples
""""""""
@ -19,48 +26,58 @@ Examples
reset_timestep 0
reset_timestep 4000000
reset_timestep 1000 time 100.0
reset_timestep NULL time 200.0
Description
"""""""""""
Set the timestep counter to the specified value. This command
normally comes after the timestep has been set by reading a restart
usually comes after the timestep has been set by reading a restart
file via the :doc:`read_restart <read_restart>` command, or a previous
simulation advanced the timestep.
simulation run or minimization advanced the timestep.
The optional *time* keyword allows to also set the accumulated
simulation time. This is usually the number of timesteps times
the size of the timestep, but when using variable size timesteps
with :doc:`fix dt/reset <fix_dt_reset>` it can differ. With
NULL as the timestep number, only the accumulated time is reset.
The :doc:`read_data <read_data>` and :doc:`create_box <create_box>`
commands set the timestep to 0; the :doc:`read_restart <read_restart>`
command sets the timestep to the value it had when the restart file
was written.
was written. The same applies to the accumulated simulation time.
Restrictions
""""""""""""
none
This command cannot be used when any fixes are defined that keep track
of elapsed time to perform certain kinds of time-dependent operations.
Examples are the :doc:`fix deposit <fix_deposit>` and :doc:`fix dt/reset <fix_dt_reset>` commands. The former adds atoms on
specific timesteps. The latter keeps track of accumulated time.
Examples are the :doc:`fix deposit <fix_deposit>` and :doc:`fix dt/reset
<fix_dt_reset>` commands. The former adds atoms on specific timesteps.
The latter keeps track of accumulated time.
Various fixes use the current timestep to calculate related
quantities. If the timestep is reset, this may produce unexpected
behavior, but LAMMPS allows the fixes to be defined even if the
timestep is reset. For example, commands which thermostat the system,
e.g. :doc:`fix nvt <fix_nh>`, allow you to specify a target temperature
which ramps from Tstart to Tstop which may persist over several runs.
If you change the timestep, you may induce an instantaneous change in
the target temperature.
Various fixes use the current timestep to calculate related quantities.
If the timestep is reset, this may produce unexpected behavior, but
LAMMPS allows the fixes to be defined even if the timestep is reset.
For example, commands which thermostat the system, e.g. :doc:`fix nvt
<fix_nh>`, allow you to specify a target temperature which ramps from
Tstart to Tstop which may persist over several runs. If you change the
timestep, you may induce an instantaneous change in the target
temperature.
Resetting the timestep clears flags for :doc:`computes <compute>` that
may have calculated some quantity from a previous run. This means
these quantity cannot be accessed by a variable in between runs until
a new run is performed. See the :doc:`variable <variable>` command for
more details.
may have calculated some quantity from a previous run. This means these
quantity cannot be accessed by a variable in between runs until a new
run is performed. See the :doc:`variable <variable>` command for more
details.
Related commands
""""""""""""""""
:doc:`rerun <rerun>`
:doc:`rerun <rerun>`, :doc:`timestep <timestep>`,
:doc:`fix dt/reset <fix_dt_reset>`
Default
"""""""

44
doc/src/set_time.rst
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@ -1,44 +0,0 @@
.. index:: set_time
set_time command
================
Syntax
""""""
.. parsed-literal::
set_time t
* t = current simulation time (time units)
Examples
""""""""
.. code-block:: LAMMPS
time 0.0
time 10.5
Description
"""""""""""
Set the current accumulated simulation time for subsequent molecular
dynamics simulations. See the :doc:`units <units>` command for the time
units associated with each choice of units that LAMMPS supports.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`reset_timestep <reset_timestep>`, :doc:`timestep <timestep>`,
:doc:`fix dt/reset <fix_dt_reset>`, :doc:`units <units>`
Default
"""""""
0.0 at the beginning of the first run.

11
src/input.cpp
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@ -773,7 +773,6 @@ int Input::execute_command()
else if (!strcmp(command,"reset_timestep")) reset_timestep();
else if (!strcmp(command,"restart")) restart();
else if (!strcmp(command,"run_style")) run_style();
else if (!strcmp(command,"set_time")) set_time();
else if (!strcmp(command,"special_bonds")) special_bonds();
else if (!strcmp(command,"suffix")) suffix();
else if (!strcmp(command,"thermo")) thermo();
@ -1773,16 +1772,6 @@ void Input::run_style()
/* ---------------------------------------------------------------------- */
void Input::set_time()
{
if (narg != 1) error->all(FLERR,"Illegal set_time command");
update->atime = utils::numeric(FLERR,arg[0],false,lmp);
update->atimestep = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void Input::special_bonds()
{
// store 1-3,1-4 and dihedral/extra flag values before change

1
src/input.h
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@ -131,7 +131,6 @@ class Input : protected Pointers {
void reset_timestep();
void restart();
void run_style();
void set_time();
void special_bonds();
void suffix();
void thermo();

16
src/update.cpp
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@ -457,9 +457,19 @@ void Update::new_minimize(char *style, int /* narg */, char ** /* arg */, int tr
void Update::reset_timestep(int narg, char **arg)
{
if (narg != 1) error->all(FLERR, "Illegal reset_timestep command");
bigint newstep = utils::bnumeric(FLERR, arg[0], false, lmp);
reset_timestep(newstep, true);
if (narg < 1) utils::missing_cmd_args(FLERR, "reset_timestep", error);
if (!utils::strmatch(arg[0], "^NULL$"))
reset_timestep(utils::bnumeric(FLERR, arg[0], false, lmp), true);
if (narg > 1) {
if (utils::strmatch(arg[1], "^time$")) {
if (narg < 3) utils::missing_cmd_args(FLERR, "reset_timestep time", error);
atimestep = ntimestep;
atime = utils::numeric(FLERR, arg[2], false, lmp);
} else
error->all(FLERR, "Unknown reset_timestep option {}", arg[1]);
}
}
/* ----------------------------------------------------------------------

40
unittest/commands/test_simple_commands.cpp
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@ -224,55 +224,43 @@ TEST_F(SimpleCommandsTest, Quit)
TEST_F(SimpleCommandsTest, ResetTimestep)
{
ASSERT_EQ(lmp->update->ntimestep, 0);
ASSERT_EQ(lmp->update->atimestep, 0);
ASSERT_DOUBLE_EQ(lmp->update->atime, 0.0);
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
ASSERT_EQ(lmp->update->atimestep, 10);
ASSERT_DOUBLE_EQ(lmp->update->atime, lmp->update->dt * 10);
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 0);
TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
}
TEST_F(SimpleCommandsTest, SetTime)
{
ASSERT_EQ(lmp->update->ntimestep, 0);
ASSERT_EQ(lmp->update->atimestep, 0);
ASSERT_DOUBLE_EQ(lmp->update->atime, 0.0);
BEGIN_HIDE_OUTPUT();
command("set_time 10.0");
command("reset_timestep NULL time 10.0");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 0);
ASSERT_EQ(lmp->update->atimestep, 0);
ASSERT_DOUBLE_EQ(lmp->update->atime, 10.0);
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
command("set_time 10.0");
command("reset_timestep 10 time 100.0");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
ASSERT_EQ(lmp->update->atimestep, 10);
ASSERT_DOUBLE_EQ(lmp->update->atime, 10.0);
ASSERT_DOUBLE_EQ(lmp->update->atime, 100.0);
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
command("set_time 10.0");
command("reset_timestep 10");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
ASSERT_EQ(lmp->update->atimestep, 10);
ASSERT_DOUBLE_EQ(lmp->update->atime, 10.0 + lmp->update->dt * 10);
TEST_FAILURE(".*ERROR: Illegal set_time .*", command("set_time"););
TEST_FAILURE(".*ERROR: Illegal set_time .*", command("set_time 10 10"););
TEST_FAILURE(".*ERROR: Expected floating .*", command("set_time xxx"););
TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
TEST_FAILURE(".*ERROR: Unknown reset_timestep option 10.*", command("reset_timestep 10 10"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 time"););
TEST_FAILURE(".*ERROR: Expected floating .**", command("reset_timestep 10 time xxx"););
TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
}
TEST_F(SimpleCommandsTest, Suffix)