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replace references to fix ave/spatial with correct equivalents

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This commit is contained in:
Axel Kohlmeyer
2024-01-21 12:24:38 -05:00
parent 722452657c
commit 6339dfad09
7 changed files with 46 additions and 46 deletions
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10
src/EXTRA-FIX/fix_viscosity.cpp
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@ -120,14 +120,14 @@ int FixViscosity::setmask()
void FixViscosity::init()
{
// warn if any fix ave/spatial comes after this fix
// warn if any fix ave/chunk comes after this fix
// can cause glitch in averaging since ave will happen after swap
int foundme = 0;
for (int i = 0; i < modify->nfix; i++) {
if (modify->fix[i] == this) foundme = 1;
if (foundme && strcmp(modify->fix[i]->style,"ave/spatial") == 0 && me == 0)
error->warning(FLERR,"Fix viscosity comes before fix ave/spatial");
for (const auto &ifix : modify->get_fix_list()) {
if (ifix == this) foundme = 1;
if (foundme && utils::strmatch(ifix->style,"^ave/chunk") && (me == 0))
error->warning(FLERR,"Fix viscosity comes before fix ave/chunk");
}
// set bounds of 2 slabs in pdim

65
src/SHOCK/fix_append_atoms.cpp
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@ -14,8 +14,6 @@
#include "fix_append_atoms.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
@ -27,11 +25,13 @@
#include "error.h"
#include "force.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
#define BIG 1.0e30
#define EPSILON 1.0e-6
static constexpr double BIG = 1.0e30;
/* ---------------------------------------------------------------------- */
@ -43,7 +43,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
next_reneighbor = -1;
time_depend = 1;
if (narg < 4) error->all(FLERR,"Illegal fix append/atoms command");
if (narg < 4) utils::missing_cmd_args(FLERR,"fix append/atoms", error);
// default settings
@ -121,8 +121,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"spatial") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix append/atoms command");
if (strcmp(arg[iarg+1],"f_") == 0)
error->all(FLERR,
"Bad fix ID in fix append/atoms command");
error->all(FLERR, "Bad fix ID in fix append/atoms command");
spatflag = 1;
spatialid = utils::strdup(arg[iarg+1]+2);
spatlead = utils::numeric(FLERR,arg[iarg+2],false,lmp);
@ -208,14 +207,14 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
FixAppendAtoms::~FixAppendAtoms()
{
delete [] basistype;
delete[] basistype;
if (ranflag) delete randomx;
if (spatflag) delete[] spatialid;
if (tempflag) {
delete randomt;
delete [] gfactor1;
delete [] gfactor2;
delete[] gfactor1;
delete[] gfactor2;
}
}
@ -239,22 +238,30 @@ void FixAppendAtoms::initial_integrate(int /*vflag*/)
/* ---------------------------------------------------------------------- */
void FixAppendAtoms::init()
{
if (spatflag) {
Fix *ifix = modify->get_fix_by_id(spatialid);
if (!ifix) error->all(FLERR,"Fix ID {} for fix ave/chunk does not exist", spatialid);
if (!utils::strmatch(ifix->style, "^ave/chunk"))
error->all(FLERR,"Fix {} for spatial keyword is not fix style ave/chunk", spatialid);}
}
/* ---------------------------------------------------------------------- */
void FixAppendAtoms::setup(int vflag)
{
/*** CALL TO CREATE GROUP? SEE POST_FORCE ***/
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
int FixAppendAtoms::get_spatial()
{
if (update->ntimestep % freq == 0) {
int ifix = modify->find_fix(spatialid);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
Fix *fix = modify->fix[ifix];
Fix *fix = modify->get_fix_by_id(spatialid);
if (!fix) error->all(FLERR,"Fix ID {} for fix ave/chunk does not exist", spatialid);
int failed = 0;
int count = 0;
@ -319,8 +326,8 @@ int FixAppendAtoms::get_spatial()
if (domain->boxhi[2] - shockfront_loc < spatlead) advance = 1;
delete [] pos;
delete [] val;
delete[] pos;
delete[] val;
}
advance_sum = 0;
@ -433,22 +440,14 @@ void FixAppendAtoms::pre_exchange()
xmin = ymin = zmin = BIG;
xmax = ymax = zmax = -BIG;
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxlo[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxlo[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxhi[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxhi[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxhi[2],xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],xmin,ymin,zmin,xmax,ymax,zmax);
int ilo,ihi,jlo,jhi,klo,khi;
ilo = static_cast<int> (xmin);

1
src/SHOCK/fix_append_atoms.h
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@ -29,6 +29,7 @@ class FixAppendAtoms : public Fix {
FixAppendAtoms(class LAMMPS *, int, char **);
~FixAppendAtoms() override;
int setmask() override;
void init() override;
void setup(int) override;
void pre_exchange() override;
void initial_integrate(int) override;

4
src/compute_centroid_stress_atom.cpp
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@ -303,8 +303,8 @@ void ComputeCentroidStressAtom::compute_peratom()
// add in per-atom contributions from relevant fixes
// skip if vatom = nullptr
// possible during setup phase if fix has not initialized its vatom yet
// e.g. fix ave/spatial defined before fix shake,
// and fix ave/spatial uses a per-atom stress from this compute as input
// e.g. fix ave/chunk defined before fix shake,
// and fix ave/chunk uses a per-atom stress from this compute as input
// fix styles are CENTROID_SAME, CENTROID_AVAIL or CENTROID_NOTAVAIL
if (fixflag) {

4
src/compute_stress_atom.cpp
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@ -216,8 +216,8 @@ void ComputeStressAtom::compute_peratom()
// add in per-atom contributions from relevant fixes
// skip if vatom = nullptr
// possible during setup phase if fix has not initialized its vatom yet
// e.g. fix ave/spatial defined before fix shake,
// and fix ave/spatial uses a per-atom stress from this compute as input
// e.g. fix ave/chunk defined before fix shake,
// and fix ave/chunk uses a per-atom stress from this compute as input
if (fixflag) {
for (auto &ifix : modify->get_fix_list())

2
src/fix_ave_chunk.cpp
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@ -485,7 +485,7 @@ void FixAveChunk::init()
/* ----------------------------------------------------------------------
only does averaging if nvalid = current timestep
do not call setup_chunks(), even though fix ave/spatial called setup_bins()
do not call setup_chunks(), even though fix ave/chunk called setup_bins()
b/c could cause nchunk to change if Nfreq epoch crosses 2 runs
does mean that if change_box is used between runs to change box size,
that nchunk may not track it

6
src/fix_ave_time.cpp
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@ -1081,17 +1081,17 @@ void FixAveTime::options(int iarg, int narg, char **arg)
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
delete[] title1;
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
delete[] title2;
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
delete[] title3;
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;