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implement set_time command

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This commit is contained in:
Axel Kohlmeyer
2022-05-03 13:15:52 -04:00
parent fef6c37ea7
commit 0bedff1ce0
10 changed files with 121 additions and 27 deletions
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1
doc/src/Commands_all.rst
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@ -105,6 +105,7 @@ 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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@ -96,6 +96,7 @@ Commands
run
run_style
set
set_time
shell
special_bonds
suffix

44
doc/src/set_time.rst Normal file
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@ -0,0 +1,44 @@
.. 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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@ -773,6 +773,7 @@ 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();
@ -1772,6 +1773,16 @@ 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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@ -131,6 +131,7 @@ class Input : protected Pointers {
void reset_timestep();
void restart();
void run_style();
void set_time();
void special_bonds();
void suffix();
void thermo();

5
src/lmprestart.h
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@ -17,7 +17,7 @@
#define MAGIC_STRING "LammpS RestartT"
#define ENDIAN 0x0001
#define ENDIANSWAP 0x1000
#define FORMAT_REVISION 2
#define FORMAT_REVISION 3
enum{VERSION,SMALLINT,TAGINT,BIGINT,
UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID,
@ -37,7 +37,8 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL,
NELLIPSOIDS,NLINES,NTRIS,NBODIES};
NELLIPSOIDS,NLINES,NTRIS,NBODIES,
ATIME,ATIMESTEP};
#define LB_FACTOR 1.1

29
src/read_restart.cpp
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@ -594,21 +594,18 @@ void ReadRestart::header()
if (flag == VERSION) {
char *version = read_string();
if (me == 0)
utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n",
version,lmp->version);
utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n", version, lmp->version);
delete[] version;
// we have no forward compatibility, thus exit with error
if (revision > FORMAT_REVISION)
error->all(FLERR,"Restart file format revision incompatible "
"with current LAMMPS version");
error->all(FLERR,"Restart file format revision incompatible with current LAMMPS version");
// warn when attempting to read older format revision
if ((me == 0) && (revision < FORMAT_REVISION))
error->warning(FLERR,"Old restart file format revision. "
"Switching to compatibility mode.");
error->warning(FLERR,"Old restart file format revision. Switching to compatibility mode.");
// check lmptype.h sizes, error if different
@ -654,8 +651,8 @@ void ReadRestart::header()
} else if (flag == NPROCS) {
nprocs_file = read_int();
if (nprocs_file != comm->nprocs && me == 0)
error->warning(FLERR,"Restart file used different # of processors: "
"{} vs. {}",nprocs_file,comm->nprocs);
error->warning(FLERR,"Restart file used different # of processors: {} vs. {}",
nprocs_file,comm->nprocs);
// don't set procgrid, warn if different
@ -681,16 +678,14 @@ void ReadRestart::header()
int newton_pair_file = read_int();
if (force->newton_pair != 1) {
if (newton_pair_file != force->newton_pair && me == 0)
error->warning(FLERR,
"Restart file used different newton pair setting, "
error->warning(FLERR, "Restart file used different newton pair setting, "
"using input script value");
}
} else if (flag == NEWTON_BOND) {
int newton_bond_file = read_int();
if (force->newton_bond != 1) {
if (newton_bond_file != force->newton_bond && me == 0)
error->warning(FLERR,
"Restart file used different newton bond setting, "
error->warning(FLERR, "Restart file used different newton bond setting, "
"using restart file value");
}
force->newton_bond = newton_bond_file;
@ -721,8 +716,7 @@ void ReadRestart::header()
boundary[2][0] != domain->boundary[2][0] ||
boundary[2][1] != domain->boundary[2][1]) {
if (me == 0)
error->warning(FLERR,
"Restart file used different boundary settings, "
error->warning(FLERR, "Restart file used different boundary settings, "
"using restart file values");
}
}
@ -864,6 +858,13 @@ void ReadRestart::header()
} else if (flag == NBODIES) {
atom->nbodies = read_bigint();
} else if (flag == ATIMESTEP) {
update->atimestep = read_bigint();
} else if (flag == ATIME) {
update->atime = read_double();
// set dimension from restart file
// for backward compatibility
} else if (flag == EXTRA_SPECIAL_PER_ATOM) {
force->special_extra = read_int();

2
src/update.h
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@ -27,7 +27,7 @@ class Update : protected Pointers {
bigint ntimestep; // current step (dynamics or min iterations)
int nsteps; // # of steps to run (dynamics or min iter)
int whichflag; // 0 for unset, 1 for dynamics, 2 for min
double atime; // simulation time at atime_step
double atime; // simulation time at atimestep
bigint atimestep; // last timestep atime was updated
bigint firststep, laststep; // 1st & last step of this run
bigint beginstep, endstep; // 1st and last step of multiple runs

20
src/write_restart.cpp
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@ -118,8 +118,7 @@ void WriteRestart::command(int narg, char **arg)
/* ---------------------------------------------------------------------- */
void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
int narg, char **arg)
void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller, int narg, char **arg)
{
multiproc = multiproc_caller;
mpiioflag = mpiioflag_caller;
@ -127,14 +126,12 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
// error checks
if (multiproc && mpiioflag)
error->all(FLERR,
"Restart file MPI-IO output not allowed with % in filename");
error->all(FLERR,"Restart file MPI-IO output not allowed with % in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
if (!mpiio->mpiio_exists)
error->all(FLERR,"Writing to MPI-IO filename when "
"MPIIO package is not installed");
error->all(FLERR,"Writing to MPI-IO filename when MPIIO package is not installed");
}
// defaults for multiproc file writing
@ -158,8 +155,7 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_restart command");
if (!multiproc)
error->all(FLERR,"Cannot use write_restart fileper "
"without % in restart file name");
error->all(FLERR,"Cannot use write_restart fileper without % in restart file name");
int nper = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nper <= 0) error->all(FLERR,"Illegal write_restart command");
@ -176,8 +172,7 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_restart command");
if (!multiproc)
error->all(FLERR,"Cannot use write_restart nfile "
"without % in restart file name");
error->all(FLERR,"Cannot use write_restart nfile without % in restart file name");
int nfile = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nfile <= 0) error->all(FLERR,"Illegal write_restart command");
nfile = MIN(nfile,nprocs);
@ -510,6 +505,11 @@ void WriteRestart::header()
write_bigint(NTRIS,atom->ntris);
write_bigint(NBODIES,atom->nbodies);
// write out current simulation time. added 3 May 2022
write_bigint(ATIMESTEP,update->atimestep);
write_double(ATIME,update->atime);
// -1 flag signals end of header
int flag = -1;

34
unittest/commands/test_simple_commands.cpp
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@ -241,6 +241,40 @@ TEST_F(SimpleCommandsTest, ResetTimestep)
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");
END_HIDE_OUTPUT();
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");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
ASSERT_EQ(lmp->update->atimestep, 10);
ASSERT_DOUBLE_EQ(lmp->update->atime, 10.0);
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_F(SimpleCommandsTest, Suffix)
{
ASSERT_EQ(lmp->suffix_enable, 0);