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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
	src/atom_vec_hybrid.cpp
	src/verlet.cpp
This commit is contained in:
Axel Kohlmeyer
2014-06-07 19:29:51 -04:00
parent cbdad2a2b3 52a1ef7a14
commit 1ee7cb100d
102 changed files with 107297 additions and 578 deletions
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104
src/atom.cpp
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@ -79,16 +79,17 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
mu = NULL;
omega = angmom = torque = NULL;
radius = rmass = NULL;
ellipsoid = line = tri = body = NULL;
vfrac = s0 = NULL;
x0 = NULL;
ellipsoid = line = tri = body = NULL;
spin = NULL;
eradius = ervel = erforce = NULL;
cs = csforce = vforce = ervelforce = NULL;
etag = NULL;
rho = drho = NULL;
e = de = NULL;
cv = NULL;
rho = drho = e = de = cv = NULL;
vest = NULL;
bond_per_atom = extra_bond_per_atom = 0;
@ -130,14 +131,19 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// initialize atom style and array existence flags
// customize by adding new flag
sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
peri_flag = electron_flag = 0;
sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = 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;
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;
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;
// Peridynamic scale factor
@ -200,6 +206,10 @@ Atom::~Atom()
memory->destroy(v);
memory->destroy(f);
memory->destroy(molecule);
memory->destroy(molindex);
memory->destroy(molatom);
memory->destroy(q);
memory->destroy(mu);
memory->destroy(omega);
@ -207,21 +217,31 @@ Atom::~Atom()
memory->destroy(torque);
memory->destroy(radius);
memory->destroy(rmass);
memory->destroy(vfrac);
memory->destroy(s0);
memory->destroy(x0);
memory->destroy(ellipsoid);
memory->destroy(line);
memory->destroy(tri);
memory->destroy(body);
memory->destroy(vfrac);
memory->destroy(s0);
memory->destroy(x0);
memory->destroy(spin);
memory->destroy(eradius);
memory->destroy(ervel);
memory->destroy(erforce);
memory->destroy(ervelforce);
memory->destroy(cs);
memory->destroy(csforce);
memory->destroy(vforce);
memory->destroy(etag);
memory->destroy(molecule);
memory->destroy(molindex);
memory->destroy(molatom);
memory->destroy(rho);
memory->destroy(drho);
memory->destroy(e);
memory->destroy(de);
memory->destroy(cv);
memory->destroy(vest);
memory->destroy(nspecial);
memory->destroy(special);
@ -250,11 +270,6 @@ Atom::~Atom()
memory->destroy(improper_atom3);
memory->destroy(improper_atom4);
// delete user-defined molecules
for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules);
// delete custom atom arrays
for (int i = 0; i < nivector; i++) {
@ -271,6 +286,11 @@ Atom::~Atom()
memory->sfree(ivector);
memory->sfree(dvector);
// delete user-defined molecules
for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules);
// delete per-type arrays
delete [] mass;
@ -320,12 +340,20 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
// may have been set by old avec
// customize by adding new flag
sphere_flag = ellipsoid_flag = line_flag = tri_flag = 0;
peri_flag = electron_flag = 0;
sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = 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;
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;
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;
// create instance of AtomVec
// use grow() to initialize atom-based arrays to length 1
@ -1867,12 +1895,34 @@ void *Atom::extract(char *name)
if (strcmp(name,"q") == 0) return (void *) q;
if (strcmp(name,"mu") == 0) return (void *) mu;
if (strcmp(name,"omega") == 0) return (void *) omega;
if (strcmp(name,"amgmom") == 0) return (void *) angmom;
if (strcmp(name,"angmom") == 0) return (void *) angmom;
if (strcmp(name,"torque") == 0) return (void *) torque;
if (strcmp(name,"radius") == 0) return (void *) radius;
if (strcmp(name,"rmass") == 0) return (void *) rmass;
if (strcmp(name,"ellipsoid") == 0) return (void *) ellipsoid;
if (strcmp(name,"line") == 0) return (void *) line;
if (strcmp(name,"tri") == 0) return (void *) tri;
if (strcmp(name,"vfrac") == 0) return (void *) vfrac;
if (strcmp(name,"s0") == 0) return (void *) s0;
if (strcmp(name,"x0") == 0) return (void *) x0;
if (strcmp(name,"spin") == 0) return (void *) spin;
if (strcmp(name,"eradius") == 0) return (void *) eradius;
if (strcmp(name,"ervel") == 0) return (void *) ervel;
if (strcmp(name,"erforce") == 0) return (void *) erforce;
if (strcmp(name,"ervelforce") == 0) return (void *) ervelforce;
if (strcmp(name,"cs") == 0) return (void *) cs;
if (strcmp(name,"csforce") == 0) return (void *) csforce;
if (strcmp(name,"vforce") == 0) return (void *) vforce;
if (strcmp(name,"etag") == 0) return (void *) etag;
if (strcmp(name,"rho") == 0) return (void *) rho;
if (strcmp(name,"drho") == 0) return (void *) drho;
if (strcmp(name,"e") == 0) return (void *) e;
if (strcmp(name,"de") == 0) return (void *) de;
if (strcmp(name,"cv") == 0) return (void *) cv;
if (strcmp(name,"vest") == 0) return (void *) vest;
return NULL;
}