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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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162
src/compute_property_atom.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -51,8 +51,8 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
pack_choice[i] = &ComputePropertyAtom::pack_id;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_molecule;
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[i] = &ComputePropertyAtom::pack_type;
@ -66,28 +66,28 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[i] = &ComputePropertyAtom::pack_z;
} else if (strcmp(arg[iarg],"xs") == 0) {
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_xs_triclinic;
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_xs_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_xs;
} else if (strcmp(arg[iarg],"ys") == 0) {
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_ys_triclinic;
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_ys_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_ys;
} else if (strcmp(arg[iarg],"zs") == 0) {
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_zs_triclinic;
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_zs_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_zs;
} else if (strcmp(arg[iarg],"xu") == 0) {
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_xu_triclinic;
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_xu_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_xu;
} else if (strcmp(arg[iarg],"yu") == 0) {
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_yu_triclinic;
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_yu_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_yu;
} else if (strcmp(arg[iarg],"zu") == 0) {
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_zu_triclinic;
if (domain->triclinic)
pack_choice[i] = &ComputePropertyAtom::pack_zu_triclinic;
else pack_choice[i] = &ComputePropertyAtom::pack_zu;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[i] = &ComputePropertyAtom::pack_ix;
@ -111,218 +111,218 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_q;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_mux;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_muy;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_muz;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_mu;
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_radius;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_diameter;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_omegax;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_omegay;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_omegaz;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_angmomx;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_angmomy;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_angmomz;
} else if (strcmp(arg[iarg],"shapex") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapex;
} else if (strcmp(arg[iarg],"shapey") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapey;
} else if (strcmp(arg[iarg],"shapez") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapez;
} else if (strcmp(arg[iarg],"quatw") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatw;
} else if (strcmp(arg[iarg],"quati") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quati;
} else if (strcmp(arg[iarg],"quatj") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatj;
} else if (strcmp(arg[iarg],"quatk") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatk;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_tqx;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_tqy;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_tqz;
} else if (strcmp(arg[iarg],"spin") == 0) {
if (!atom->spin_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_spin;
} else if (strcmp(arg[iarg],"eradius") == 0) {
if (!atom->eradius_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_eradius;
} else if (strcmp(arg[iarg],"ervel") == 0) {
if (!atom->ervel_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_ervel;
} else if (strcmp(arg[iarg],"erforce") == 0) {
if (!atom->erforce_flag)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_erforce;
} else if (strcmp(arg[iarg],"end1x") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end1x;
} else if (strcmp(arg[iarg],"end1y") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end1y;
} else if (strcmp(arg[iarg],"end1z") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end1z;
} else if (strcmp(arg[iarg],"end2x") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end2x;
} else if (strcmp(arg[iarg],"end2y") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end2y;
} else if (strcmp(arg[iarg],"end2z") == 0) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_end2z;
} else if (strcmp(arg[iarg],"corner1x") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner1x;
} else if (strcmp(arg[iarg],"corner1y") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner1y;
} else if (strcmp(arg[iarg],"corner1z") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner1z;
} else if (strcmp(arg[iarg],"corner2x") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner2x;
} else if (strcmp(arg[iarg],"corner2y") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner2y;
} else if (strcmp(arg[iarg],"corner2z") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner2z;
} else if (strcmp(arg[iarg],"corner3x") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner3x;
} else if (strcmp(arg[iarg],"corner3y") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner3y;
} else if (strcmp(arg[iarg],"corner3z") == 0) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_corner3z;
} else error->all(FLERR,"Invalid keyword in compute property/atom command");
@ -572,9 +572,9 @@ void ComputePropertyAtom::pack_xs_triclinic(int n)
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
if (mask[i] & groupbit)
buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
else buf[n] = 0.0;
n += nvalues;
}
@ -630,7 +630,7 @@ void ComputePropertyAtom::pack_xu(int n)
double xprd = domain->xprd;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (mask[i] & groupbit)
buf[n] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
else buf[n] = 0.0;
n += nvalues;