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changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution

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This commit is contained in:
Steve Plimpton
2017-03-21 08:56:37 -06:00
parent 145e682ad3
commit dcede304df
112 changed files with 912 additions and 534 deletions
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74
src/fix_external.cpp
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@ -36,6 +36,7 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
virial_flag = 1;
extscalar = 1;
if (strcmp(arg[3],"pf/callback") == 0) {
@ -80,6 +81,7 @@ int FixExternal::setmask()
{
int mask = 0;
if (mode == PF_CALLBACK || mode == PF_ARRAY) {
mask |= PRE_REVERSE;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= MIN_POST_FORCE;
@ -102,6 +104,13 @@ void FixExternal::setup(int vflag)
post_force(vflag);
}
/* --------------------------------------------------------------------- */
void FixExternal::setup_pre_reverse(int eflag, int vflag)
{
pre_reverse(eflag,vflag);
}
/* ---------------------------------------------------------------------- */
void FixExternal::min_setup(int vflag)
@ -109,12 +118,25 @@ void FixExternal::min_setup(int vflag)
post_force(vflag);
}
/* ----------------------------------------------------------------------
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
void FixExternal::pre_reverse(int eflag, int vflag)
{
eflag_caller = eflag;
}
/* ---------------------------------------------------------------------- */
void FixExternal::post_force(int vflag)
{
bigint ntimestep = update->ntimestep;
int eflag = eflag_caller;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
// invoke the callback in driver program
// it will fill fexternal with forces
@ -145,11 +167,57 @@ void FixExternal::min_post_force(int vflag)
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
caller invokes this method to set its contribution to global energy
do not just return if eflag_global is not set
input script could access this quantity via compute_scalar()
even if eflag is not set on a particular timestep
------------------------------------------------------------------------- */
void FixExternal::set_energy(double eng)
void FixExternal::set_energy_global(double caller_energy)
{
user_energy = eng;
user_energy = caller_energy;
}
/* ----------------------------------------------------------------------
caller invokes this method to set its contribution to global virial
------------------------------------------------------------------------- */
void FixExternal::set_virial_global(double *caller_virial)
{
if (!vflag_global) return;
for (int i = 0; i < 6; i++)
virial[i] = caller_virial[i];
}
/* ----------------------------------------------------------------------
caller invokes this method to set its contribution to peratom energy
------------------------------------------------------------------------- */
void FixExternal::set_energy_peratom(double *caller_energy)
{
if (!eflag_atom) return;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
eatom[i] = caller_energy[i];
}
/* ----------------------------------------------------------------------
caller invokes this method to set its contribution to peratom virial
------------------------------------------------------------------------- */
void FixExternal::set_virial_peratom(double **caller_virial)
{
int i,j;
if (!vflag_atom) return;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
for (j = 0; j < 6; j++)
vatom[i][j] = caller_virial[i][j];
}
/* ----------------------------------------------------------------------