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Moving temp/heat keywords out of dump to compute prop/atom

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This commit is contained in:
jtclemm
2024-02-23 14:31:40 -07:00
parent fef2150bfb
commit dd4cd240df
10 changed files with 64 additions and 63 deletions
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5
doc/src/Howto_granular.rst
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@ -45,10 +45,15 @@ atoms, and should be used for granular system instead of the fix style
To model heat conduction, one must add the temperature and heatflow
atom variables with:
* :doc:`fix property/atom <fix_property_atom>`
a temperature integration fix
* :doc:`fix heat/flow <fix_heat_flow>`
and a heat conduction option defined in both
* :doc:`pair_style granular <pair_granular>`
* :doc:`fix wall/gran <fix_wall_gran>`

5
doc/src/compute_property_atom.rst
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@ -23,8 +23,9 @@ Syntax
spx, spy, spz, sp, fmx, fmy, fmz,
nbonds,
radius, diameter, omegax, omegay, omegaz,
temperature, heatflow,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
shapex, shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
@ -56,6 +57,8 @@ Syntax
*nbonds* = number of bonds assigned to an atom
*radius,diameter* = radius,diameter of spherical particle
*omegax,omegay,omegaz* = angular velocity of spherical particle
*temperature* = internal temperature of spherical particle
*heatflow* = internal heat flow of spherical particle
*angmomx,angmomy,angmomz* = angular momentum of aspherical particle
*shapex,shapey,shapez* = 3 diameters of aspherical particle
*quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles

3
doc/src/dump.rst
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@ -104,7 +104,6 @@ Syntax
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
heatflow, temperature,
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
i_name, d_name, i2_name[I], d2_name[I]
@ -131,8 +130,6 @@ Syntax
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
heatflow = rate of heat flow into particle
temperature = temperature of particle
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID

17
doc/src/fix_property_atom.rst
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@ -22,6 +22,8 @@ Syntax
*mol* = molecule IDs
*q* = charge
*rmass* = per-atom mass
*temperature* = internal temperature of atom
*heatflow* = internal heat flow of atom
i_name = new integer vector referenced by name
d_name = new floating-point vector referenced by name
i2_name = new integer array referenced by name
@ -59,14 +61,18 @@ these properties for each atom in the system when a data file is read.
This fix augments the set of per-atom properties with new custom
ones. This can be useful in several scenarios.
If the atom style does not define molecule IDs, per-atom charge, or
per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
If the atom style does not define molecule IDs, per-atom charge,
per-atom mass, internal temperature, or internal heat flow, they can
be added using the *mol*\ , *q*, *rmass*, *temperature*, or *heatflow*
keywords. This could be useful to define "molecules" to use as rigid
bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
around an extra flag with atoms (stored as a molecule ID) that can be
used by various commands like :doc:`compute chunk/atom
<compute_chunk_atom>` to group atoms without having to use the group
command (which is limited to a total of 32 groups including *all*\ ).
For finite-size particles, an internal temperature and heat flow can
be used to model heat conduction as in the
:doc:`GRANULAR package <Howto_granular>`.
Another application is to use the *rmass* flag in order to have
per-atom masses instead of per-type masses. This could be used to
@ -85,9 +91,10 @@ properties that are not needed such as bond lists, which incurs some
overhead when there are no bonds.
In the future, we may add additional existing per-atom properties to
fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
"turn-on" specific properties defined by some atom styles, so they can
be easily used by atom styles that do not define them.
fix property/atom, similar to *mol*\ , *q*, *rmass*\ , *temperature*\ ,
or *heatflow* which "turn-on" specific properties defined by some atom
styles, so they can be easily used by atom styles that do not define
them.
More generally, the *i_name* and *d_name* options allow one or more
new custom per-atom vectors to be defined. Likewise the *i2_name* and

3
examples/granular/in.pour.heat
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@ -73,7 +73,8 @@ thermo 100
timestep 0.001
#dump 1 all custom 1000 ${name}.dump id type radius mass x y z temperature heatflow
compute 1 all property/atom temperature heatflow
#dump 1 all custom 1000 ${name}.dump id type radius mass x y z c_1[*]
run 100000

2
src/BPM/bond_bpm.cpp
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@ -357,7 +357,6 @@ void BondBPM::process_broken(int i, int j)
if (i < nlocal) {
for (m = 0; m < num_bond[i]; m++) {
if (bond_atom[i][m] == tag[j]) {
bond_type[i][m] = 0;
n = num_bond[i];
bond_type[i][m] = bond_type[i][n - 1];
bond_atom[i][m] = bond_atom[i][n - 1];
@ -372,7 +371,6 @@ void BondBPM::process_broken(int i, int j)
if (j < nlocal) {
for (m = 0; m < num_bond[j]; m++) {
if (bond_atom[j][m] == tag[i]) {
bond_type[j][m] = 0;
n = num_bond[j];
bond_type[j][m] = bond_type[j][n - 1];
bond_atom[j][m] = bond_atom[j][n - 1];

38
src/compute_property_atom.cpp
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@ -205,6 +205,14 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (!atom->omega_flag)
error->all(FLERR,"Compute property/atom {} is not available", arg[iarg]);
pack_choice[i] = &ComputePropertyAtom::pack_omegaz;
} else if (strcmp(arg[iarg],"temperature") == 0) {
if (!atom->temperature_flag)
error->all(FLERR,"Compute property/atom {} is not available", arg[iarg]);
pack_choice[i] = &ComputePropertyAtom::pack_temperature;
} else if (strcmp(arg[iarg],"heatflow") == 0) {
if (!atom->heatflow_flag)
error->all(FLERR,"Compute property/atom {} is not available", arg[iarg]);
pack_choice[i] = &ComputePropertyAtom::pack_heatflow;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Compute property/atom {} is not available", arg[iarg]);
@ -1213,6 +1221,36 @@ void ComputePropertyAtom::pack_omegaz(int n)
/* ---------------------------------------------------------------------- */
void ComputePropertyAtom::pack_temperature(int n)
{
double *temperature = atom->temperature;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = temperature[i];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyAtom::pack_heatflow(int n)
{
double *heatflow = atom->heatflow;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = heatflow[i];
else buf[n] = 0.0;
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputePropertyAtom::pack_angmomx(int n)
{
double **angmom = atom->angmom;

2
src/compute_property_atom.h
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@ -95,6 +95,8 @@ class ComputePropertyAtom : public Compute {
void pack_omegax(int);
void pack_omegay(int);
void pack_omegaz(int);
void pack_temperature(int);
void pack_heatflow(int);
void pack_angmomx(int);
void pack_angmomy(int);
void pack_angmomz(int);

50
src/dump_custom.cpp
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@ -41,7 +41,7 @@ enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS,
XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,HEATFLOW,TEMPERATURE,
Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
TQX,TQY,TQZ,
COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY};
@ -929,18 +929,6 @@ int DumpCustom::count()
for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == HEATFLOW) {
if (!atom->heatflow_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = atom->heatflow;
nstride = 1;
} else if (thresh_array[ithresh] == TEMPERATURE) {
if (!atom->temperature_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = atom->temperature;
nstride = 1;
} else if (thresh_array[ithresh] == OMEGAX) {
if (!atom->omega_flag)
error->all(FLERR,
@ -1395,16 +1383,6 @@ int DumpCustom::parse_fields(int narg, char **arg)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[iarg] = &DumpCustom::pack_diameter;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"heatflow") == 0) {
if (!atom->heatflow_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[iarg] = &DumpCustom::pack_heatflow;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"temperature") == 0) {
if (!atom->temperature_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[iarg] = &DumpCustom::pack_temperature;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
@ -1875,8 +1853,6 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"radius") == 0) thresh_array[nthresh] = RADIUS;
else if (strcmp(arg[1],"diameter") == 0) thresh_array[nthresh] = DIAMETER;
else if (strcmp(arg[1],"heatflow") == 0) thresh_array[nthresh] = HEATFLOW;
else if (strcmp(arg[1],"temperature") == 0) thresh_array[nthresh] = TEMPERATURE;
else if (strcmp(arg[1],"omegax") == 0) thresh_array[nthresh] = OMEGAX;
else if (strcmp(arg[1],"omegay") == 0) thresh_array[nthresh] = OMEGAY;
else if (strcmp(arg[1],"omegaz") == 0) thresh_array[nthresh] = OMEGAZ;
@ -2791,30 +2767,6 @@ void DumpCustom::pack_diameter(int n)
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_heatflow(int n)
{
double *heatflow = atom->heatflow;
for (int i = 0; i < nchoose; i++) {
buf[n] = heatflow[clist[i]];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_temperature(int n)
{
double *temperature = atom->temperature;
for (int i = 0; i < nchoose; i++) {
buf[n] = temperature[clist[i]];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_omegax(int n)
{
double **omega = atom->omega;

2
src/dump_custom.h
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@ -188,8 +188,6 @@ class DumpCustom : public Dump {
void pack_mu(int);
void pack_radius(int);
void pack_diameter(int);
void pack_heatflow(int);
void pack_temperature(int);
void pack_omegax(int);
void pack_omegay(int);