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reformat

This commit is contained in:
Axel Kohlmeyer 2021-06-22 18:29:13 -04:00
parent cc7538e7b9
commit f5f5721cfb
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GPG Key ID: D9B44E93BF0C375A
1 changed files with 73 additions and 65 deletions
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138
src/fix_dt_reset.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -14,21 +13,22 @@
#include "fix_dt_reset.h" #include "fix_dt_reset.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "dump.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "integrate.h"
#include "lattice.h"
#include "modify.h"
#include "output.h"
#include "pair.h"
#include "update.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
#include "atom.h"
#include "update.h"
#include "integrate.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "pair.h"
#include "modify.h"
#include "fix.h"
#include "output.h"
#include "dump.h"
#include "comm.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
@ -37,10 +37,9 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) : FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
Fix(lmp, narg, arg)
{ {
if (narg < 7) error->all(FLERR,"Illegal fix dt/reset command"); if (narg < 7) error->all(FLERR, "Illegal fix dt/reset command");
// set time_depend, else elapsed time accumulation can be messed up // set time_depend, else elapsed time accumulation can be messed up
@ -51,40 +50,47 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) :
extvector = 0; extvector = 0;
dynamic_group_allow = 1; dynamic_group_allow = 1;
nevery = utils::inumeric(FLERR,arg[3],false,lmp); nevery = utils::inumeric(FLERR, arg[3], false, lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix dt/reset command"); if (nevery <= 0) error->all(FLERR, "Illegal fix dt/reset command");
minbound = maxbound = 1; minbound = maxbound = 1;
tmin = tmax = 0.0; tmin = tmax = 0.0;
if (strcmp(arg[4],"NULL") == 0) minbound = 0; if (strcmp(arg[4], "NULL") == 0)
else tmin = utils::numeric(FLERR,arg[4],false,lmp); minbound = 0;
if (strcmp(arg[5],"NULL") == 0) maxbound = 0; else
else tmax = utils::numeric(FLERR,arg[5],false,lmp); tmin = utils::numeric(FLERR, arg[4], false, lmp);
xmax = utils::numeric(FLERR,arg[6],false,lmp); if (strcmp(arg[5], "NULL") == 0)
maxbound = 0;
else
tmax = utils::numeric(FLERR, arg[5], false, lmp);
xmax = utils::numeric(FLERR, arg[6], false, lmp);
if (minbound && tmin < 0.0) error->all(FLERR,"Illegal fix dt/reset command"); if (minbound && tmin < 0.0) error->all(FLERR, "Illegal fix dt/reset command");
if (maxbound && tmax < 0.0) error->all(FLERR,"Illegal fix dt/reset command"); if (maxbound && tmax < 0.0) error->all(FLERR, "Illegal fix dt/reset command");
if (minbound && maxbound && tmin >= tmax) if (minbound && maxbound && tmin >= tmax) error->all(FLERR, "Illegal fix dt/reset command");
error->all(FLERR,"Illegal fix dt/reset command"); if (xmax <= 0.0) error->all(FLERR, "Illegal fix dt/reset command");
if (xmax <= 0.0) error->all(FLERR,"Illegal fix dt/reset command");
int scaleflag = 1; int scaleflag = 1;
emax = -1.0; emax = -1.0;
int iarg = 7; int iarg = 7;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) { if (strcmp(arg[iarg], "units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix dt/reset command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal fix dt/reset command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; if (strcmp(arg[iarg + 1], "box") == 0)
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; scaleflag = 0;
else error->all(FLERR,"Illegal fix dt/reset command"); else if (strcmp(arg[iarg + 1], "lattice") == 0)
scaleflag = 1;
else
error->all(FLERR, "Illegal fix dt/reset command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"emax") == 0) { } else if (strcmp(arg[iarg], "emax") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix dt/reset command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal fix dt/reset command");
emax = utils::numeric(FLERR,arg[iarg+1],false,lmp); emax = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
if (emax <= 0.0) error->all(FLERR,"Illegal fix dt/reset command"); if (emax <= 0.0) error->all(FLERR, "Illegal fix dt/reset command");
iarg += 2; iarg += 2;
} else error->all(FLERR,"Illegal fix dt/reset command"); } else
error->all(FLERR, "Illegal fix dt/reset command");
} }
// setup scaling, based on xlattice parameter // setup scaling, based on xlattice parameter
@ -113,15 +119,15 @@ void FixDtReset::init()
// set rRESPA flag // set rRESPA flag
respaflag = 0; respaflag = 0;
if (utils::strmatch(update->integrate_style,"^respa")) respaflag = 1; if (utils::strmatch(update->integrate_style, "^respa")) respaflag = 1;
// check for DCD or XTC dumps // check for DCD or XTC dumps
for (int i = 0; i < output->ndump; i++) for (int i = 0; i < output->ndump; i++)
if ((strcmp(output->dump[i]->style,"dcd") == 0 || if ((strcmp(output->dump[i]->style, "dcd") == 0 ||
strcmp(output->dump[i]->style,"xtc") == 0) && comm->me == 0) strcmp(output->dump[i]->style, "xtc") == 0) &&
error->warning(FLERR, comm->me == 0)
"Dump dcd/xtc timestamp may be wrong with fix dt/reset"); error->warning(FLERR, "Dump dcd/xtc timestamp may be wrong with fix dt/reset");
ftm2v = force->ftm2v; ftm2v = force->ftm2v;
mvv2e = force->mvv2e; mvv2e = force->mvv2e;
@ -139,9 +145,9 @@ void FixDtReset::setup(int /*vflag*/)
void FixDtReset::end_of_step() void FixDtReset::end_of_step()
{ {
double dtv,dtf,dte,dtsq; double dtv, dtf, dte, dtsq;
double vsq,fsq,massinv; double vsq, fsq, massinv;
double delx,dely,delz,delr; double delx, dely, delz, delr;
double **v = atom->v; double **v = atom->v;
double **f = atom->f; double **f = atom->f;
@ -155,31 +161,33 @@ void FixDtReset::end_of_step()
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (rmass) massinv = 1.0/rmass[i]; if (rmass)
else massinv = 1.0/mass[type[i]]; massinv = 1.0 / rmass[i];
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; else
fsq = f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2]; massinv = 1.0 / mass[type[i]];
vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2];
dtv = dtf = dte = BIG; dtv = dtf = dte = BIG;
if (vsq > 0.0) dtv = xmax/sqrt(vsq); if (vsq > 0.0) dtv = xmax / sqrt(vsq);
if (fsq > 0.0) dtf = sqrt(2.0*xmax/(ftm2v*sqrt(fsq)*massinv)); if (fsq > 0.0) dtf = sqrt(2.0 * xmax / (ftm2v * sqrt(fsq) * massinv));
dt = MIN(dtv,dtf); dt = MIN(dtv, dtf);
if (emax > 0.0 && vsq > 0.0 && fsq > 0.0) { if (emax > 0.0 && vsq > 0.0 && fsq > 0.0) {
dte = emax/sqrt(fsq*vsq)/sqrt(ftm2v*mvv2e); dte = emax / sqrt(fsq * vsq) / sqrt(ftm2v * mvv2e);
dt = MIN(dt, dte); dt = MIN(dt, dte);
} }
dtsq = dt*dt; dtsq = dt * dt;
delx = dt*v[i][0] + 0.5*dtsq*massinv*f[i][0] * ftm2v; delx = dt * v[i][0] + 0.5 * dtsq * massinv * f[i][0] * ftm2v;
dely = dt*v[i][1] + 0.5*dtsq*massinv*f[i][1] * ftm2v; dely = dt * v[i][1] + 0.5 * dtsq * massinv * f[i][1] * ftm2v;
delz = dt*v[i][2] + 0.5*dtsq*massinv*f[i][2] * ftm2v; delz = dt * v[i][2] + 0.5 * dtsq * massinv * f[i][2] * ftm2v;
delr = sqrt(delx*delx + dely*dely + delz*delz); delr = sqrt(delx * delx + dely * dely + delz * delz);
if (delr > xmax) dt *= xmax/delr; if (delr > xmax) dt *= xmax / delr;
dtmin = MIN(dtmin,dt); dtmin = MIN(dtmin, dt);
} }
MPI_Allreduce(&dtmin,&dt,1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&dtmin, &dt, 1, MPI_DOUBLE, MPI_MIN, world);
if (minbound) dt = MAX(dt,tmin); if (minbound) dt = MAX(dt, tmin);
if (maxbound) dt = MIN(dt,tmax); if (maxbound) dt = MIN(dt, tmax);
// if timestep didn't change, just return // if timestep didn't change, just return
// else reset update->dt and other classes that depend on it // else reset update->dt and other classes that depend on it