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Extra D2min options/checks for undercoord particles

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This commit is contained in:
jtclemm
2024-04-23 20:58:20 -06:00
parent 80a0c5899e
commit 3dbfe26b6d
3 changed files with 64 additions and 14 deletions
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15
doc/src/fix_nonaffine_displacement.rst
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
fix ID group nonaffine/displacement style args reference/style nstep
fix ID group nonaffine/displacement style args reference/style nstep keyword values
* ID, group are documented in :doc:`fix <fix>` command
* nonaffine/displacement = style name of this fix command
@ -32,6 +32,13 @@ Syntax
*update* = update the reference frame every *nstep* timesteps
*offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement
* zero or more keyword/value pairs may be appended
.. parsed-literal::
*z/min* values = zmin
zmin = minimum coordination number to calculate D2min
Examples
""""""""
@ -76,6 +83,12 @@ is the identity tensor. This calculation is only performed on timesteps that
are a multiple of *nevery* (including timestep zero). Data accessed before
this occurs will simply be zeroed.
For particles with low coordination numbers, calculations of :math:`D^2_\mathrm{min}`
may have poor accuracy. An optional minimum coordination number can be defined using
the *z/min* keyword. If any particles have fewer than the specified number of particles
in the cutoff distance or in contact, the above calculations will be skipped and the
peratom array entries will be zero.
The *integrated* style simply integrates the velocity of particles
every timestep to calculate a displacement. This style only works if
used in conjunction with another fix that deforms the box and displaces

59
src/EXTRA-FIX/fix_nonaffine_displacement.cpp
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@ -46,6 +46,8 @@ enum { TYPE, RADIUS, CUSTOM };
enum { INTEGRATED, D2MIN };
enum { FIXED, OFFSET, UPDATE };
static constexpr double EPSILON = 1.0e-15;
static const char cite_nonaffine_d2min[] =
"@article{PhysRevE.57.7192,\n"
" title = {Dynamics of viscoplastic deformation in amorphous solids},\n"
@ -66,7 +68,7 @@ static const char cite_nonaffine_d2min[] =
FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), id_fix(nullptr), fix(nullptr), D2min(nullptr), X(nullptr), Y(nullptr),
F(nullptr), norm(nullptr)
F(nullptr), norm(nullptr), singular(nullptr)
{
if (narg < 4) utils::missing_cmd_args(FLERR,"fix nonaffine/displacement", error);
@ -74,6 +76,8 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char *
if (nevery <= 0) error->all(FLERR,"Illegal nevery value {} in fix nonaffine/displacement", nevery);
reference_timestep = update_timestep = offset_timestep = -1;
z_min = 0;
int iarg = 4;
if (strcmp(arg[iarg], "integrated") == 0) {
nad_style = INTEGRATED;
@ -117,6 +121,16 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char *
if ((offset_timestep <= 0) || (offset_timestep > nevery))
error->all(FLERR, "Illegal offset timestep {} in fix nonaffine/displacement", arg[iarg + 1]);
} else error->all(FLERR,"Illegal reference style {} in fix nonaffine/displacement", arg[iarg]);
iarg += 2;
while (iarg < narg) {
if (strcmp(arg[iarg], "z/min") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR,"fix nonaffine/displacement", error);
z_min = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (z_min < 0) error->all(FLERR, "Minimum coordination must be positive");
iarg += 2;
} else error->all(FLERR,"Illegal keyword {} in fix nonaffine/displacement", arg[iarg]);
}
if (nad_style == D2MIN)
if (cut_style == RADIUS && (!atom->radius_flag))
@ -151,6 +165,7 @@ FixNonaffineDisplacement::~FixNonaffineDisplacement()
memory->destroy(Y);
memory->destroy(F);
memory->destroy(norm);
memory->destroy(singular);
memory->destroy(D2min);
}
@ -395,6 +410,7 @@ void FixNonaffineDisplacement::calculate_D2Min()
}
}
norm[i] = 0;
singular[i] = 0;
D2min[i] = 0;
}
@ -471,14 +487,29 @@ void FixNonaffineDisplacement::calculate_D2Min()
}
if (dim == 3) {
invert3(Y_tmp, Y_inv);
denom = det3(Y_tmp);
if (fabs(denom) < EPSILON) {
singular[i] = 1;
for (j = 0; j < 3; j++)
for (k = 0; k < 3; k++)
Y_inv[j][k] = 0.0;
} else {
invert3(Y_tmp, Y_inv);
}
} else {
denom = Y_tmp[0][0] * Y_tmp[1][1] - Y_tmp[0][1] * Y_tmp[1][0];
if (denom != 0.0) denom = 1.0 / denom;
Y_inv[0][0] = Y_tmp[1][1] * denom;
Y_inv[0][1] = -Y_tmp[0][1] * denom;
Y_inv[1][0] = -Y_tmp[1][0] * denom;
Y_inv[1][1] = Y_tmp[0][0] * denom;
if (fabs(denom) < EPSILON) {
singular[i] = 1;
for (j = 0; j < 2; j++)
for (k = 0; k < 2; k++)
Y_inv[j][k] = 0.0;
} else {
denom = 1.0 / denom;
Y_inv[0][0] = Y_tmp[1][1] * denom;
Y_inv[0][1] = -Y_tmp[0][1] * denom;
Y_inv[1][0] = -Y_tmp[1][0] * denom;
Y_inv[1][1] = Y_tmp[0][0] * denom;
}
}
times3(X_tmp, Y_inv, F_tmp);
@ -559,10 +590,14 @@ void FixNonaffineDisplacement::calculate_D2Min()
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (norm[i] != 0)
D2min[i] /= norm[i];
else
D2min[i] = 0.0;
if (norm[i] < z_min || singular[i] == 1) {
array_atom[i][0] = 0.0;
array_atom[i][1] = 0.0;
array_atom[i][2] = 0.0;
continue;
}
D2min[i] /= norm[i];
for (j = 0; j < 3; j++)
for (k = 0; k < 3; k++)
@ -743,10 +778,12 @@ void FixNonaffineDisplacement::grow_arrays(int nmax_new)
memory->destroy(F);
memory->destroy(D2min);
memory->destroy(norm);
memory->destroy(singular);
memory->create(X, nmax, 3, 3, "fix_nonaffine_displacement:X");
memory->create(Y, nmax, 3, 3, "fix_nonaffine_displacement:Y");
memory->create(F, nmax, 3, 3, "fix_nonaffine_displacement:F");
memory->create(D2min, nmax, "fix_nonaffine_displacement:D2min");
memory->create(norm, nmax, "fix_nonaffine_displacement:norm");
memory->create(singular, nmax, "fix_nonaffine_displacement:singular");
}
}

4
src/EXTRA-FIX/fix_nonaffine_displacement.h
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@ -48,12 +48,12 @@ class FixNonaffineDisplacement : public Fix {
int nmax, comm_flag;
int nad_style, cut_style;
int reference_style, offset_timestep, reference_timestep, update_timestep;
int reference_saved;
int reference_saved, z_min;
double cutoff_custom, cutsq_custom, mycutneigh;
double xprd0, yprd0, zprd0, xprd0_half, yprd0_half, zprd0_half, xy0, xz0, yz0;
double *D2min, ***X, ***Y, ***F;
int *norm;
int *norm, *singular;
class NeighList *list; // half neighbor list