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add optional nmax keyword to fix vector to allow using it as a sliding window

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This commit is contained in:
Axel Kohlmeyer
2023-07-22 00:08:17 -04:00
parent a4a206e601
commit a48f4597a2
3 changed files with 55 additions and 25 deletions
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41
doc/src/fix_vector.rst
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@ -8,11 +8,12 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID vector Nevery value1 value2 ...
fix ID group-ID vector Nevery [nmax <length>] value1 value2 ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* vector = style name of this fix command
* Nevery = use input values every this many timesteps
* nmax <length> = set maximal length of vector to <length> (optional)
* one or more input values can be listed
* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
@ -32,6 +33,7 @@ Examples
fix 1 all vector 100 c_myTemp
fix 1 all vector 5 c_myTemp v_integral
fix 1 all vector 50 nmax 200 c_myTemp
Description
"""""""""""
@ -43,6 +45,10 @@ values, they are stored as rows in a global array, whose number of
rows is growing. The resulting vector or array can be used by other
:doc:`output commands <Howto_output>`.
The optional *nmax* keyword can be used to restrict the length of the
vector to the given *length* value. Once the vector is filled, the
oldest entries will be discarded when new entries are added.
One way to to use this command is to accumulate a vector that is
time-integrated using the :doc:`variable trap() <variable>` function.
For example the velocity auto-correlation function (VACF) can be
@ -94,11 +100,12 @@ calculated by the compute is used.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix vector. Or it can be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
can thus be accessed by fix vector. Or it can be a compute defined not
in your input script, but by :doc:`thermodynamic output <thermo_style>`
or other fixes such as :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale
<fix_temp_rescale>`. See the doc pages for these commands which give
the IDs of these computes. Users can also write code for their own
compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
@ -108,7 +115,8 @@ calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
Users can also write code for their own fix styles and :doc:`add them to
LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. An equal-style or
@ -126,8 +134,9 @@ quantities to be stored by fix vector.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix produces a global vector or global array which can be
accessed by various :doc:`output commands <Howto_output>`. The values
@ -144,15 +153,15 @@ the vector are "intensive" or "extensive". If the fix produces an
array, then all elements in the array must be the same, either
"intensive" or "extensive". If a compute or fix provides the value
stored, then the compute or fix determines whether the value is
intensive or extensive; see the page for that compute or fix for
further info. Values produced by a variable are treated as intensive.
intensive or extensive; see the page for that compute or fix for further
info. Values produced by a variable are treated as intensive.
This fix can allocate storage for stored values accumulated over
multiple runs, using the *start* and *stop* keywords of the
:doc:`run <run>` command. See the :doc:`run <run>` command for details of
how to do this. If using the :doc:`run pre no <run>` command option,
this is required to allow the fix to allocate sufficient storage for
stored values.
multiple runs, using the *start* and *stop* keywords of the :doc:`run
<run>` command. See the :doc:`run <run>` command for details of how to
do this. If using the :doc:`run pre no <run>` command option, this is
required to allow the fix to allocate sufficient storage for stored
values.
This fix is not invoked during :doc:`energy minimization <minimize>`.

36
src/fix_vector.cpp
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@ -35,10 +35,20 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
if (nevery <= 0) error->all(FLERR, "Invalid fix vector every argument: {}", nevery);
nmaxval = MAXSMALLINT;
nindex = 0;
int iarg = 4;
if (strcmp(arg[iarg], "nmax") == 0) {
nmaxval = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (nmaxval < 1) error->all(FLERR, "Invalid nmax value");
iarg += 2;
}
// parse values
values.clear();
for (int iarg = 4; iarg < narg; iarg++) {
while (iarg < narg) {
ArgInfo argi(arg[iarg]);
value_t val;
@ -51,6 +61,7 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR, "Invalid fix vector argument: {}", arg[iarg]);
values.push_back(val);
++iarg;
}
// setup and error check
@ -132,7 +143,7 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
vector = nullptr;
array = nullptr;
ncount = ncountmax = 0;
ncount = ncountmax = nindex = 0;
if (values.size() == 1)
size_vector = 0;
else
@ -199,6 +210,7 @@ void FixVector::init()
bigint finalstep = update->endstep / nevery * nevery;
if (finalstep > update->endstep) finalstep -= nevery;
ncountmax = (finalstep - initialstep) / nevery + 1;
if (ncountmax > nmaxval) ncountmax = nmaxval;
if (values.size() == 1)
memory->grow(vector, ncountmax, "vector:vector");
else
@ -221,16 +233,18 @@ void FixVector::end_of_step()
// skip if not step which requires doing something
if (update->ntimestep != nextstep) return;
if (ncount == ncountmax) error->all(FLERR, "Overflow of allocated fix vector storage");
// wrap around when vector/array is full
nindex = ncount % ncountmax;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
double *result;
if (values.size() == 1)
result = &vector[ncount];
result = &vector[nindex];
else
result = array[ncount];
result = array[nindex];
modify->clearstep_compute();
@ -290,9 +304,9 @@ void FixVector::end_of_step()
ncount++;
if (values.size() == 1)
size_vector++;
size_vector = MIN(size_vector + 1, ncountmax);
else
size_array_rows++;
size_array_rows = MIN(size_array_rows + 1, ncountmax);
}
/* ----------------------------------------------------------------------
@ -301,7 +315,9 @@ void FixVector::end_of_step()
double FixVector::compute_vector(int i)
{
return vector[i];
int idx = i;
if (ncount >= ncountmax) idx = (i + ncount) % ncountmax;
return vector[idx];
}
/* ----------------------------------------------------------------------
@ -310,5 +326,7 @@ double FixVector::compute_vector(int i)
double FixVector::compute_array(int i, int j)
{
return array[i][j];
int idx = i;
if (ncount >= ncountmax) idx = (i + ncount) % ncountmax;
return array[idx][j];
}

3
src/fix_vector.h
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@ -52,6 +52,9 @@ class FixVector : public Fix {
int ncount; // # of values currently in growing vector or array
int ncountmax; // max # of values vector/array can hold
int nmaxval; // maximum allowed number of values
int nindex; // start index of data, may wrap around
double *vector;
double **array;
};