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enable replicate to work with local ptrs

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This commit is contained in:
Steve Plimpton
2019-12-18 08:56:03 -07:00
parent db6d272303
commit b6374bacfb
47 changed files with 686 additions and 480 deletions
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83
src/atom.cpp
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@ -175,42 +175,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
iname = dname = NULL;
// initialize atom style and array existence flags
// customize by adding new flag
sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = 0;
q_flag = mu_flag = 0;
omega_flag = torque_flag = angmom_flag = 0;
radius_flag = rmass_flag = 0;
ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
// magnetic flags
sp_flag = 0;
vfrac_flag = 0;
spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
dpd_flag = edpd_flag = tdpd_flag = 0;
// USER-SMD
smd_flag = 0;
contact_radius_flag = 0;
smd_data_9_flag = 0;
smd_stress_flag = 0;
x0_flag = 0;
eff_plastic_strain_flag = 0;
eff_plastic_strain_rate_flag = 0;
damage_flag = 0;
// Peridynamic scale factor
pdscale = 1.0;
set_atomflag_defaults();
// initialize peratom data structure
@ -668,6 +634,32 @@ void Atom::add_peratom_vary(const char *name, void *address,
nperatom++;
}
/* ----------------------------------------------------------------------
add info for a single per-atom array to PerAtom data struct
customize by adding new flag, identical list as atom.h 2nd customization
------------------------------------------------------------------------- */
void Atom::set_atomflag_defaults()
{
sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = molindex_flag = molatom_flag = 0;
q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = ervelforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
dpd_flag = edpd_flag = tdpd_flag = 0;
sp_flag = 0;
x0_flag = 0;
smd_flag = damage_flag = 0;
contact_radius_flag = smd_data_9_flag = smd_stress_flag = 0;
eff_plastic_strain_flag = eff_plastic_strain_rate_flag = 0;
pdscale = 1.0;
}
/* ----------------------------------------------------------------------
create an AtomVec style
called from lammps.cpp, input script, restart file, replicate
@ -682,26 +674,8 @@ void Atom::create_avec(const char *style, int narg, char **arg, int trysuffix)
// unset atom style and array existence flags
// may have been set by old avec
// customize by adding new flag
sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = 0;
q_flag = mu_flag = 0;
omega_flag = torque_flag = angmom_flag = 0;
radius_flag = rmass_flag = 0;
ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
// magnetic flags
sp_flag = 0;
vfrac_flag = 0;
spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
set_atomflag_defaults();
// create instance of AtomVec
// use grow() to initialize atom-based arrays to length 1
@ -785,6 +759,7 @@ AtomVec *Atom::avec_creator(LAMMPS *lmp)
return new T(lmp);
}
/* ---------------------------------------------------------------------- */
void Atom::init()