Merge pull request from rbberger/gran-wall-store-contacts-fix

Document and fix store_contacts in fix gran/wall and gran/wall/region
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Axel Kohlmeyer 2020-06-11 18:04:23 -04:00 committed by GitHub
commit fc9bbd4d06
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5 changed files with 98 additions and 18 deletions

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@ -45,7 +45,7 @@ Syntax
radius = cylinder radius (distance units)
* zero or more keyword/value pairs may be appended to args
* keyword = *wiggle* or *shear*
* keyword = *wiggle* or *shear* or *contacts*
.. parsed-literal::
@ -56,6 +56,9 @@ Syntax
*shear* values = dim vshear
dim = *x* or *y* or *z*
vshear = magnitude of shear velocity (velocity units)
*contacts* value = none
generate contact information for each particle
Examples
""""""""
@ -68,6 +71,7 @@ Examples
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
fix 6 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
Description
"""""""""""
@ -171,6 +175,7 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
*vshear* < 0. In this case, *vshear* is the tangential velocity of
the wall at whatever *radius* has been defined.
**Restart, fix_modify, output, run start/stop, minimize info:**
This fix writes the shear friction state of atoms interacting with the
@ -181,11 +186,37 @@ info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
If the :code:`contacts` option is used, this fix generates a per-atom array
with 8 columns as output, containing the contact information for owned
particles (nlocal on each processor). All columns in this per-atom array will
be zero if no contact has occurred. The values of these columns are listed in
the following table:
+-------+----------------------------------------------------+----------------+
| Index | Value | Units |
+=======+====================================================+================+
| 1 | 1.0 if particle is in contact with wall, | |
| | 0.0 otherwise | |
+-------+----------------------------------------------------+----------------+
| 2 | Force :math:`f_x` exerted on the wall | force units |
+-------+----------------------------------------------------+----------------+
| 3 | Force :math:`f_y` exerted on the wall | force units |
+-------+----------------------------------------------------+----------------+
| 4 | Force :math:`f_z` exerted on the wall | force units |
+-------+----------------------------------------------------+----------------+
| 5 | :math:`\Delta x` between wall surface and particle | distance units |
+-------+----------------------------------------------------+----------------+
| 6 | :math:`\Delta y` between wall surface and particle | distance units |
+-------+----------------------------------------------------+----------------+
| 7 | :math:`\Delta z` between wall surface and particle | distance units |
+-------+----------------------------------------------------+----------------+
| 8 | Radius :math:`r` of atom | distance units |
+-------+----------------------------------------------------+----------------+
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
No parameter of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy
minimization <minimize>`.
Restrictions
""""""""""""

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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID
fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* wall/region = style name of this fix command
@ -36,6 +36,12 @@ Syntax
* wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
* region-ID = region whose boundary will act as wall
* keyword = *contacts*
.. parsed-literal::
*contacts* value = none
generate contact information for each particle
Examples
""""""""
@ -46,6 +52,7 @@ Examples
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone contacts
Description
"""""""""""
@ -215,11 +222,37 @@ uninterrupted fashion.
use the same fix ID for fix wall/gran/region, but assign it a region
with a different region ID.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
If the :code:`contacts` option is used, this fix generates a per-atom array
with 8 columns as output, containing the contact information for owned
particles (nlocal on each processor). All columns in this per-atom array will
be zero if no contact has occurred. The values of these columns are listed in
the following table:
+-------+----------------------------------------------------+----------------+
| Index | Value | Units |
+=======+====================================================+================+
| 1 | 1.0 if particle is in contact with wall, | |
| | 0.0 otherwise | |
+-------+----------------------------------------------------+----------------+
| 2 | Force :math:`f_x` exerted on the wall | force units |
+-------+----------------------------------------------------+----------------+
| 3 | Force :math:`f_y` exerted on the wall | force units |
+-------+----------------------------------------------------+----------------+
| 4 | Force :math:`f_z` exerted on the wall | force units |
+-------+----------------------------------------------------+----------------+
| 5 | :math:`\Delta x` between wall surface and particle | distance units |
+-------+----------------------------------------------------+----------------+
| 6 | :math:`\Delta y` between wall surface and particle | distance units |
+-------+----------------------------------------------------+----------------+
| 7 | :math:`\Delta z` between wall surface and particle | distance units |
+-------+----------------------------------------------------+----------------+
| 8 | Radius :math:`r` of atom | distance units |
+-------+----------------------------------------------------+----------------+
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
No parameter of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy
minimization <minimize>`.
Restrictions
""""""""""""

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@ -370,7 +370,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
vshear = force->numeric(FLERR,arg[iarg+2]);
wshear = 1;
iarg += 3;
} else if (strcmp(arg[iarg],"store_contacts") == 0) {
} else if (strcmp(arg[iarg],"contacts") == 0) {
peratom_flag = 1;
size_peratom_cols = 8;
peratom_freq = 1;
@ -426,10 +426,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
}
if (peratom_flag) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < size_peratom_cols; m++)
array_atom[i][m] = 0.0;
clear_stored_contacts();
}
time_origin = update->ntimestep;
@ -596,6 +593,10 @@ void FixWallGran::post_force(int /*vflag*/)
rwall = 0.0;
if (peratom_flag) {
clear_stored_contacts();
}
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -668,7 +669,7 @@ void FixWallGran::post_force(int /*vflag*/)
// store contact info
if (peratom_flag) {
array_atom[i][0] = (double)atom->tag[i];
array_atom[i][0] = 1.0;
array_atom[i][4] = x[i][0] - dx;
array_atom[i][5] = x[i][1] - dy;
array_atom[i][6] = x[i][2] - dz;
@ -702,6 +703,15 @@ void FixWallGran::post_force(int /*vflag*/)
}
}
void FixWallGran::clear_stored_contacts() {
const int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
for (int m = 0; m < size_peratom_cols; m++) {
array_atom[i][m] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void FixWallGran::post_force_respa(int vflag, int ilevel, int /*iloop*/)

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@ -110,6 +110,8 @@ class FixWallGran : public Fix {
// store particle interactions
int store;
void clear_stored_contacts();
};
}

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@ -178,6 +178,10 @@ void FixWallGranRegion::post_force(int /*vflag*/)
region->set_velocity();
}
if (peratom_flag) {
clear_stored_contacts();
}
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) continue;