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Fixing various memory issues

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This commit is contained in:
jtclemm
2023-04-26 12:14:40 -06:00
parent be568d257d
commit 0cd3bd190f
10 changed files with 127 additions and 34 deletions
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83
examples/PACKAGES/rheo/poiseuille/in.rheo.poiseuille Normal file
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@ -0,0 +1,83 @@
dimension 2
units lj
atom_style rheo
boundary p p p
comm_modify vel yes
# ------ Particle Lattice/Resolution Parameters ------ #
variable L equal 10
variable sf equal 0.2
variable n equal 1.0/(${sf}^2)
variable cut equal 3.5*${sf}
# ------ Create simulation box ------ #
region box block 0 20 -10 10 -0.01 0.01 units box
create_box 2 box
lattice sq ${n}
region topwall block INF INF 7 10 INF INF units box
region block block INF INF -6.99 6.99 INF INF units box
region botwall block INF INF -10 -7 INF INF units box
create_atoms 2 region topwall
create_atoms 2 region botwall
create_atoms 1 region block
group fluid type 1
group rig type 2
variable dr equal 0.1*${sf}
displace_atoms fluid random $(0.1*v_sf) ${dr} 0 135414 units box
# ------ Model parameters ------ #
variable rho0 equal 1.0
variable cs equal 1.0
variable mp equal ${rho0}/${n}
variable zeta equal 1.0
variable kappa equal 1.0*${rho0}/${mp}
variable fext equal 1e-3/${n}
variable eta equal 0.1
variable dt_max equal 0.1*${cut}/${cs}/3
variable Dr equal 0.05*${cut}*${cs}
mass 1 ${mp}
mass 2 ${mp}
set group all rheo/rho ${rho0}
set group all rheo/status 0
set group rig rheo/status 2
timestep ${dt_max}
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
pair_coeff * *
# ------ Fixes & computes ------ #
fix 1 all rheo ${cut} Quintic 0 shift
fix 2 all rheo/viscosity constant ${eta}
fix 3 all rheo/pressure linear
fix 4 rig setforce 0.0 0.0 0.0
fix 5 fluid addforce ${fext} 0.0 0.0
compute 1 all rheo/property/atom rho phase
# ------ Output & Run ------ #
thermo 200
thermo_style custom step time temp press
variable skin equal 0.2*${cut}
neighbor ${skin} bin
neigh_modify one 5000
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_1[*]
run 20000

42
src/RHEO/compute_rheo_kernel.cpp
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@ -103,10 +103,6 @@ void ComputeRHEOKernel::init()
{
neighbor->add_request(this, NeighConst::REQ_FULL);
auto fixes = modify->get_fix_by_style("rheo");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use compute rheo/kernel");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
interface_flag = fix_rheo->interface_flag;
compute_interface = fix_rheo->compute_interface;
@ -147,17 +143,16 @@ void ComputeRHEOKernel::init_list(int /*id*/, NeighList *ptr)
int ComputeRHEOKernel::check_corrections(int i)
{
int corrections = 1;
if (gsl_error_flag) {
// If there were errors, check to see if it occured for this atom
// Skip if there were gsl errors for this atom
if (gsl_error_flag)
if (gsl_error_tags.find(atom->tag[i]) != gsl_error_tags.end())
corrections = 0;
}
return 0;
if (coordination[i] < zmin) corrections = 0;
// Skip if undercoordinated
if (coordination[i] < zmin)
return 0;
return corrections;
return 1;
}
/* ---------------------------------------------------------------------- */
@ -165,12 +160,17 @@ int ComputeRHEOKernel::check_corrections(int i)
double ComputeRHEOKernel::calc_w(int i, int j, double delx, double dely, double delz, double r)
{
double w;
int corrections_i, corrections_j, corrections;
int corrections_i = check_corrections(i);
int corrections_j = check_corrections(j);
int corrections = corrections_i & corrections_j;
if (kernel_style != QUINTIC) {
corrections_i = check_corrections(i);
corrections_j = check_corrections(j);
corrections = corrections_i & corrections_j;
} else {
corrections = 0;
}
if (kernel_style == QUINTIC || !corrections) w = calc_w_quintic(i,j,delx,dely,delz,r);
if (!corrections) w = calc_w_quintic(i,j,delx,dely,delz,r);
else if (kernel_style == CRK0) w = calc_w_crk0(i,j,delx,dely,delz,r);
else if (kernel_style == CRK1) w = calc_w_crk1(i,j,delx,dely,delz,r);
else if (kernel_style == CRK2) w = calc_w_crk2(i,j,delx,dely,delz,r);
@ -183,14 +183,18 @@ double ComputeRHEOKernel::calc_w(int i, int j, double delx, double dely, double
double ComputeRHEOKernel::calc_dw(int i, int j, double delx, double dely, double delz, double r)
{
double wp;
int corrections_i, corrections_j;
int corrections_i = check_corrections(i);
int corrections_j = check_corrections(j);
if (kernel_style != QUINTIC) {
corrections_i = check_corrections(i);
corrections_j = check_corrections(j);
}
// Calc wp and default dW's, a bit inefficient but can redo later
wp = calc_dw_quintic(i,j,delx,dely,delz,r,dWij,dWji);
// Overwrite if there are corrections
if (kernel_style == CRK1) {
//check if kernel correction calculated successfully. If not, revert to quintic
if (corrections_i) calc_dw_crk1(i,j,delx,dely,delz,r,dWij);
if (corrections_j) calc_dw_crk1(j,i,-delx,-dely,-delz,r,dWji);
} else if (kernel_style == CRK2) {

4
src/RHEO/compute_rheo_property_atom.cpp
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@ -52,7 +52,7 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
if (nvalues == 1) size_peratom_cols = 0;
else size_peratom_cols = nvalues;
thermal_flag, interface_flag, surface_flag, shift_flag = 0;
thermal_flag = interface_flag = surface_flag = shift_flag = 0;
// parse input values
// customize a new keyword by adding to if statement
@ -132,7 +132,7 @@ ComputeRHEOPropertyAtom::~ComputeRHEOPropertyAtom()
void ComputeRHEOPropertyAtom::init()
{
auto fixes = modify->get_fix_by_style("rheo");
auto fixes = modify->get_fix_by_style("^rheo$");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);

4
src/RHEO/fix_rheo.cpp
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@ -195,7 +195,7 @@ void FixRHEO::init()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (modify->get_fix_by_style("rheo").size() > 1)
if (modify->get_fix_by_style("^rheo$").size() > 1)
error->all(FLERR,"Can only specify one instance of fix rheo");
}
@ -258,6 +258,8 @@ void FixRHEO::setup(int /*vflag*/)
error->one(FLERR, "Fix rheo/viscosity does not fully cover all atoms");
if (!t_coverage_flag)
error->one(FLERR, "Fix rheo/thermal does not fully cover all atoms");
pre_force(0);
}
/* ---------------------------------------------------------------------- */

4
src/RHEO/fix_rheo_pressure.cpp
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@ -92,7 +92,7 @@ int FixRHEOPressure::setmask()
void FixRHEOPressure::init()
{
auto fixes = modify->get_fix_by_style("rheo");
auto fixes = modify->get_fix_by_style("^rheo$");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/pressure");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
@ -161,7 +161,7 @@ void FixRHEOPressure::pre_force(int /*vflag*/)
}
}
if (last_flag && comm_forward) comm->forward_comm(this);
if (comm_forward) comm->forward_comm(this);
}
/* ---------------------------------------------------------------------- */

1
src/RHEO/fix_rheo_pressure.h
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@ -41,7 +41,6 @@ class FixRHEOPressure : public Fix {
double c_cubic, csq, rho0, rho0inv;
double *pressure;
int pressure_style;
int first_flag, last_flag;
int nmax_store;
class FixRHEO *fix_rheo;

2
src/RHEO/fix_rheo_thermal.cpp
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@ -155,7 +155,7 @@ int FixRHEOThermal::setmask()
void FixRHEOThermal::init()
{
auto fixes = modify->get_fix_by_style("rheo");
auto fixes = modify->get_fix_by_style("^rheo$");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);

2
src/RHEO/fix_rheo_viscosity.cpp
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@ -102,7 +102,7 @@ int FixRHEOViscosity::setmask()
void FixRHEOViscosity::init()
{
auto fixes = modify->get_fix_by_style("rheo");
auto fixes = modify->get_fix_by_style("^rheo$");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);

11
src/RHEO/pair_rheo.cpp
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@ -356,7 +356,9 @@ void PairRHEO::settings(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
int iarg = 0;
h = utils::numeric(FLERR,arg[0],false,lmp);
printf("settings\n");
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg], "rho/damp") == 0) {
if (iarg + 1 >= narg) error->all(FLERR,"Illegal pair_style command");
@ -419,10 +421,13 @@ void PairRHEO::setup()
compute_grad = fix_rheo->compute_grad;
compute_interface = fix_rheo->compute_interface;
thermal_flag = fix_rheo->thermal_flag;
h = fix_rheo->h;
csq = fix_rheo->csq;
rho0 = fix_rheo->rho0;
printf("setup\n");
if (h != fix_rheo->h)
error->all(FLERR, "Pair rheo cutoff {} does not agree with fix rheo cutoff {}", h, fix_rheo->h);
hsq = h * h;
hinv = 1.0 / h;
hinv3 = hinv * 3.0;
cs = sqrt(csq);
@ -450,6 +455,6 @@ double PairRHEO::init_one(int i, int j)
if (setflag[i][j] == 0) {
error->all(FLERR,"All pair rheo coeffs are not set");
}
printf("init one\n");
return h;
}

4
src/compute_rheo_property_atom.cpp
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@ -52,7 +52,7 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a
if (nvalues == 1) size_peratom_cols = 0;
else size_peratom_cols = nvalues;
thermal_flag, interface_flag, surface_flag, shift_flag = 0;
thermal_flag = interface_flag = surface_flag = shift_flag = 0;
// parse input values
// customize a new keyword by adding to if statement
@ -132,7 +132,7 @@ ComputeRHEOPropertyAtom::~ComputeRHEOPropertyAtom()
void ComputeRHEOPropertyAtom::init()
{
auto fixes = modify->get_fix_by_style("rheo");
auto fixes = modify->get_fix_by_style("^rheo$");
if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/viscosity");
fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);