diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 95ec350e12..a310f9f868 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -8,11 +8,12 @@ Syntax .. code-block:: LAMMPS - fix ID group-ID vector Nevery value1 value2 ... + fix ID group-ID vector Nevery [nmax ] value1 value2 ... * ID, group-ID are documented in :doc:`fix ` command * vector = style name of this fix command * Nevery = use input values every this many timesteps +* nmax = set maximal length of vector to (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 `. +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() ` 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 ` 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 ` or other fixes such as :doc:`fix nvt ` -or :doc:`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 `. +can thus be accessed by fix vector. Or it can be a compute defined not +in your input script, but by :doc:`thermodynamic output ` +or other fixes such as :doc:`fix nvt ` or :doc:`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 `. 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 `. +Users can also write code for their own fix styles and :doc:`add them to +LAMMPS `. 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 `. None of the :doc:`fix_modify ` options -are relevant to this fix. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`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 `. 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 ` command. See the :doc:`run ` command for details of -how to do this. If using the :doc:`run pre no ` 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 +` command. See the :doc:`run ` command for details of how to +do this. If using the :doc:`run pre no ` 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 `. diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 6d561a58df..fde24b716c 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -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]; } diff --git a/src/fix_vector.h b/src/fix_vector.h index 5d29492aa8..7f5394702c 100644 --- a/src/fix_vector.h +++ b/src/fix_vector.h @@ -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; };