void GLGPUDataset::SerializeDataInfoToString(std::string& buf) const
{
#if WITH_PROTOBUF
PBDataInfo pb;
pb.set_model(PBDataInfo::GLGPU);
pb.set_name(_data_name);
if (Lengths()[0]>0) {
pb.set_ox(Origins()[0]);
pb.set_oy(Origins()[1]);
pb.set_oz(Origins()[2]);
pb.set_lx(Lengths()[0]);
pb.set_ly(Lengths()[1]);
pb.set_lz(Lengths()[2]);
}
pb.set_bx(B()[0]);
pb.set_by(B()[1]);
pb.set_bz(B()[2]);
pb.set_kex(Kex());
pb.set_dx(dims()[0]);
pb.set_dy(dims()[1]);
pb.set_dz(dims()[2]);
pb.set_pbc_x(pbc()[0]);
pb.set_pbc_y(pbc()[0]);
pb.set_pbc_z(pbc()[0]);
pb.SerializeToString(&buf);
#endif
}
void ApplyPerBoundaries(void) {
size_t i;
for(i=0; i<(nA+nB); i++) {
rx[i] += pbc(rx[i]);
ry[i] += pbc(ry[i]);
}
}
void force_LJ(mdsys_t *sys)
{
double rsq,ffac;
double rx,ry,rz;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i,j;
int natoms=sys->natoms;
/* zero energy and forces */
sys->epot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
for(i=0; i < natoms-1; ++i) {
for(j=i+1; j < natoms; ++j) {
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(sys->rx[i] - sys->rx[j], b);
ry=pbc(sys->ry[i] - sys->ry[j], b);
rz=pbc(sys->rz[i] - sys->rz[j], b);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
double rsqinv = 1/rsq;
double r6 = rsqinv*rsqinv*rsqinv;
double pr = p*r6;
double p6 = 4.0*sys->epsilon*pr;
double p12 = p6*pr;
ffac = rsqinv*(12*p12-6*p6);
sys->epot += 0.5*(p12-p6);
sys->fx[i] += rx*ffac;
sys->fy[i] += ry*ffac;
sys->fz[i] += rz*ffac;
sys->fx[j] -= rx*ffac;
sys->fy[j] -= ry*ffac;
sys->fz[j] -= rz*ffac;
}
}
}
}
void force_morse(mdsys_t *sys)
{
double rsq,ffac;
double rx,ry,rz;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i,j;
int natoms=sys->natoms;
/* zero energy and forces */
sys->epot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
for(i=0; i < natoms-1; ++i) {
for(j=i+1; j < natoms; ++j) {
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(sys->rx[i] - sys->rx[j], b);
ry=pbc(sys->ry[i] - sys->ry[j], b);
rz=pbc(sys->rz[i] - sys->rz[j], b);
rsq = rx*rx + ry*ry + rz*rz;
rs = sqrt(rsqi);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
esp = exp((-1)*sys->a*(rs-sys->rzero));
espq = exp((-1)*sys->a*(rs-sys->rzero)*(rs-sys->rzero));
ffac = 2*sys->De * (1-esp)*sys->a*esp;
sys->epot += sys->De*(1-espq)
sys->fx[i] += rx*ffac;
sys->fy[i] += ry*ffac;
sys->fz[i] += rz*ffac;
sys->fx[j] -= rx*ffac;
sys->fy[j] -= ry*ffac;
sys->fz[j] -= rz*ffac;
}
}
}
}
static int send_broadcast(t_server *server, t_player *player, t_list tmp,
char *params)
{
t_player *tmp_player;
int tile;
char buffer[4096];
unsigned int i;
i = -1;
while (++i < list_get_size(tmp))
{
if ((tmp_player = list_get_elem_at_position(tmp, i)) != NULL
&& tmp_player->sock != player->sock)
{
tile = determine_best_way(server, player, tmp_player);
if (memset(buffer, 0, 1024) == NULL
|| snprintf(buffer, 1024, BROADCAST,
tile, params) == -1)
return (-1);
if (store_answer_p(tmp_player, strdup(buffer), 0) == -1)
return (-1);
}
}
return (pbc(server, player));
}
int main (int argc, char *argv[]) {
double frce;
input();
inithydro();
equili();
initpop();
for (istep = 1; istep <= nsteps; istep++) {
pbc();
mbc();
move();
hydrovar();
equili();
collis();
if (iforce)
force(istep, &frce);
if (iobst)
obst();
if (istep % ndiag == 0)
diag0D();
if (istep % nout == 0)
profil(istep, frce);
}
return 0;
}
std::vector<ElemIdType> GLGPU3DDataset::GetNeighborIds(ElemIdType elem_id) const
{
std::vector<ElemIdType> neighbors;
int idx[3], idx1[3];
ElemId2Idx(elem_id, idx);
for (int face=0; face<6; face++) {
switch (face) {
case 0: idx1[0] = idx[0]; idx1[1] = idx[1]; idx1[2] = idx[2]-1; break;
case 1: idx1[0] = idx[0]-1; idx1[1] = idx[1]; idx1[2] = idx[2]; break;
case 2: idx1[0] = idx[0]; idx1[1] = idx[1]-1; idx1[2] = idx[2]; break;
case 3: idx1[0] = idx[0]; idx1[1] = idx[1]; idx1[2] = idx[2]+1; break;
case 4: idx1[0] = idx[0]+1; idx1[1] = idx[1]; idx1[2] = idx[2]; break;
case 5: idx1[0] = idx[0]; idx1[1] = idx[1]+1; idx1[2] = idx[2]; break;
default: break;
}
#if 0 // pbc
for (int i=0; i<3; i++)
if (pbc()[i]) {
idx1[i] = idx1[i] % dims()[i];
if (idx1[i]<0) idx1[i] += dims()[i];
}
#endif
neighbors.push_back(Idx2ElemId(idx1));
}
return neighbors;
}
void MakeList(void) {
size_t i, j, k, n, jcell;
double rxi, ryi;
double rxij, ryij, r2;
Np = 0;
for(k=0; k<(nCells*nCells); k++) {
i = head[k];
rxi = rx[i];
ryi = ry[i];
while (i != (nA+nB+1)) {
j = head[k];
while (j != (nA+nB+1)) {
rxij = rxi-rx[j];
ryij = ryi-ry[j];
rxij += pbc(rxij);
ryij += pbc(ryij);
r2 = rxij*rxij+ryij*ryij;
if (r2 < (Rbuf*Rbuf)) {
ipair[Np] = i;
jpair[Np] = j;
Np++;
}
j = list[j];
}
/* now neighboring cells */
for(n=0; n<4; n++) {
jcell = map[4*k+n];
j = head[jcell];
while (j != (nA+nB+1)) {
rxij = rxi-rx[j];
ryij = ryi-ry[j];
rxij += pbc(rxij);
ryij += pbc(ryij);
r2 = rxij*rxij+ryij*ryij;
if (r2 < (Rbuf*Rbuf)) {
ipair[Np] = i;
jpair[Np] = j;
Np++;
}
j = list[j];
}
}
i = list[i];
}
}
}
void Bubble:: raw_initialize()
{
Tracer *p = root;
for( size_t i=size;i>0;--i,p=p->next )
{
pbc(p->vertex);
const Tracer *q = p->next; assert(q!=NULL);
Vertex pq(p->vertex,q->vertex);
pbc(pq);
p->edge = pq;
p->s2 = p->edge.norm2();
p->s = Sqrt( p->s2 );
}
compute_area();
content = pressure * area;
compute_geometry();
}
int setup_simulation_box(FILE* finput, system_t* system) {
// read in input.pqr molecules
system->molecules = read_molecules(finput, system);
if (!system->molecules && system->ensemble == ENSEMBLE_REPLAY) {
output(
"INPUT: end of trajectory file\n");
return 1;
} else if (!system->molecules) {
error(
"INPUT: error reading in input molecules\n");
return (-1);
} else
output(
"INPUT: finished reading in molecules\n");
//read in pqr box and calculate periodic boundary conditions if neccessary
if (system->read_pqr_box_on)
read_pqr_box(finput, system);
pbc(system);
if (system->ensemble != ENSEMBLE_SURF && system->ensemble != ENSEMBLE_SURF_FIT) {
if ((system->pbc->volume <= 0.0) || (system->pbc->cutoff <= 0.0)) {
error(
"INPUT: invalid simulation box dimensions.\n");
return -1;
;
}
}
if (system->pbc->volume > 0)
printboxdim(system->pbc);
// read in the insertion molecules
if (system->insert_input) {
system->insertion_molecules = read_insertion_molecules(system);
if (!system->insertion_molecules) {
error(
"INPUT: error read in insertion molecules\n");
return -1;
} else
output(
"INPUT: finished reading in insertion molecules\n");
} else //else only 1 sorbate type
system->sorbateCount = 1;
// now that we've read in the sorbates, we can check that user_fugacities is properly set (if used)
if (system->user_fugacities) {
if (system->fugacitiesCount != system->sorbateCount) {
error(
"INPUT: number of fugacities set via user_fugacities does not match the number of sorbates.\n");
return -1;
}
}
return 0;
}
void gfx_player_broadcast(t_ctrl *c, t_player *p, char *s)
{
t_jm_list *l;
l = c->l;
while (l)
{
if (l->fd != -1 && l->data && ((t_handler *)l->data)->t == GFX)
pbc(l, p->id, s);
l = l->next;
}
}
/* compute forces */
void force(mdsys_t *sys)
{
double r,ffac;
double rx,ry,rz;
int i,j;
/* zero energy and forces */
sys->epot=0.0;
azzero(sys->fx,sys->natoms);
azzero(sys->fy,sys->natoms);
azzero(sys->fz,sys->natoms);
for(i=0; i < (sys->natoms); ++i) {
for(j=0; j < (sys->natoms); ++j) {
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(sys->rx[i] - sys->rx[j], 0.5*sys->box);
ry=pbc(sys->ry[i] - sys->ry[j], 0.5*sys->box);
rz=pbc(sys->rz[i] - sys->rz[j], 0.5*sys->box);
r = sqrt(rx*rx + ry*ry + rz*rz);
/* compute force and energy if within cutoff */
if (r < sys->rcut) {
ffac = -4.0*sys->epsilon*(-12.0*pow(sys->sigma/r,12.0)/r
+6*pow(sys->sigma/r,6.0)/r);
sys->epot += 0.5*4.0*sys->epsilon*(pow(sys->sigma/r,12.0)
-pow(sys->sigma/r,6.0));
sys->fx[i] += rx/r*ffac;
sys->fy[i] += ry/r*ffac;
sys->fz[i] += rz/r*ffac;
}
}
}
}
void ComputeForces(void) {
size_t i, j, k;
double pot;
double rxij, ryij, r2, r6, Rc;
#pragma omp parallel for
for(i=0; i<(nA+nB); i++) { /* reset forces */
fx[i] = 0.0;
fy[i] = 0.0;
}
Epot = 0.0;
P = 0.0;
#pragma omp parallel for
for(k=0; k<Np; k++) { /* loop over all pairs */
i = ipair[k];
j = jpair[k];
rxij = rx[i]-rx[j];
ryij = ry[j]-ry[j];
rxij += pbc(rxij);
ryij += pbc(ryij);
r2 = rxij*rxij+ryij*ryij;
Rc = Rcut(i, j);
if (r2 > Rc*Rc) {
r2 = 1.0/r2;
r6 = r2*r2*r2;
Epot += r6*(r6-1.0);
P += r6*(r6-0.5);
pot = r2*r6*(r6-0.5);
fx[i] += rxij*pot;
fy[i] += ryij*pot;
fx[j] -= rxij*pot;
fy[j] -= ryij*pot;
}
}
Epot *= 4.0;
}
/* scale the volume : used in NPT ensemble */
void volume_change(system_t *system) {
molecule_t *m;
atom_t *a;
double new_volume, log_new_volume, basis_scale_factor;
double new_com[3], old_com[3], delta_pos[3];
int i, j;
// figure out what the new volume will be
if (system->ensemble == ENSEMBLE_REPLAY)
//if ensemble replay, then we're just trying to calculate the pressure via dV change
new_volume = system->pbc->volume + system->calc_pressure_dv;
else {
log_new_volume = log(system->pbc->volume) + (get_rand(system) - 0.5) * system->volume_change_factor;
new_volume = exp(log_new_volume);
}
//scale basis
basis_scale_factor = pow(new_volume / system->pbc->volume, 1.0 / 3.0);
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
system->pbc->basis[i][j] *= basis_scale_factor;
//recalculate PBC stuff (volume/reciprocal basis/cutoff)
pbc(system);
system->observables->volume = system->pbc->volume;
//scale molecule positions
for (m = system->molecules; m; m = m->next) {
for (i = 0; i < 3; i++) {
old_com[i] = m->com[i]; //molecule ptr's com will be udated during pairs routine
new_com[i] = m->com[i] * basis_scale_factor;
delta_pos[i] = new_com[i] - old_com[i];
}
for (a = m->atoms; a; a = a->next) { //calculate new atomic positions based on new com
for (i = 0; i < 3; i++) {
a->pos[i] += delta_pos[i];
a->wrapped_pos[i] += delta_pos[i];
}
}
}
return;
}
void find(int now,int i,int cur)
{
int temp=i;
if(now>bound)
return;
if(cur==4)
{
i++;
}
for(;i<=9;i++)
{
if(!flag)
{
step[now]=i;
pfc(i);
flag=Is();
find(now+1,i,temp==i?(cur+1):2);
pbc(i);
}
}
}
/* revert changes to volume */
void revert_volume_change(system_t *system) {
double basis_scale_factor, new_volume;
double old_com[3], new_com[3], delta_pos[3];
molecule_t *m;
atom_t *a;
int i, j;
new_volume = system->checkpoint->observables->volume;
//un-scale basis
basis_scale_factor = pow(new_volume / system->pbc->volume, 1.0 / 3.0); //system->pbc->volume still has rejected value until pbc() is called
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
system->pbc->basis[i][j] *= basis_scale_factor;
//recalc PBC stuff
pbc(system);
system->observables->volume = system->pbc->volume;
//scale molecule positions
for (m = system->molecules; m; m = m->next) {
for (i = 0; i < 3; i++) {
old_com[i] = m->com[i]; //molecule ptr's com will ned to be updated since this is a revert (no energy call following)
new_com[i] = m->com[i] * basis_scale_factor;
m->com[i] = new_com[i];
delta_pos[i] = new_com[i] - old_com[i];
}
for (a = m->atoms; a; a = a->next) { //calculate new atomic positions based on new com
for (i = 0; i < 3; i++) {
a->pos[i] += delta_pos[i];
a->wrapped_pos[i] += delta_pos[i];
}
}
}
wrapall(system->molecules, system->pbc);
return;
}
/* compute forces */
void force(mdsys_t *sys)
{
double r_c2 = sys->rcut * sys->rcut;
double c1, c2, c3, c4, sig6;
double epot;
int i;
/* zero energy and forces */
epot=0.0;
azzero(sys->fx,sys->natoms);
azzero(sys->fy,sys->natoms);
azzero(sys->fz,sys->natoms);
/* Precalculate some of the constants used in the potential */
sig6 = (sys->sigma)*(sys->sigma)*(sys->sigma) * (sys->sigma)*(sys->sigma)*(sys->sigma);
c1 = -24.0 * sys->epsilon * sig6;
c2 = 48.0 * sys->epsilon * sig6 * sig6;
c3 = -4.0 * sys->epsilon * sig6; // Leading 4.0 includes factor 2
c4 = 4.0 * sys->epsilon * sig6 * sig6; // for using Newton's 3rd law (Epot)
#ifdef _OPENMP
#pragma omp parallel for private(i) reduction(+:epot)
#endif
for(i=0; i < (sys->natoms); ++i) {
int j;
double r6;
double rxi, ryi, rzi;
double fx, fy, fz;
fx = fy = fz = 0.0;
rxi = sys->rx[i];
ryi = sys->ry[i];
rzi = sys->rz[i];
for(j=i+1; j < (sys->natoms); ++j) {
double rx, ry, rz;
double r2, ffac;
/* get distance between particle i and j */
rx = pbc(rxi - sys->rx[j], 0.5*sys->box);
ry = pbc(ryi - sys->ry[j], 0.5*sys->box);
rz = pbc(rzi - sys->rz[j], 0.5*sys->box);
r2 = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (r2 < r_c2) {
r6 = r2*r2*r2;
ffac = (c2 + c1*r6) / (r6*r6*r2);
epot += (c4 + c3*r6) / (r6*r6);
/*
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fx[i] += rx*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fy[i] += ry*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fz[i] += rz*ffac;
*/
fx += rx*ffac;
fy += ry*ffac;
fz += rz*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fx[j] -= rx*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fy[j] -= ry*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fz[j] -= rz*ffac;
}
} /* end loop j */
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fx[i] += fx;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fy[i] += fy;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fz[i] += fz;
} /* end loop i */
sys->epot = epot;
}
int main() {
// Floating point precision
typedef double FLOAT;
// Units
typedef angstrom<FLOAT> x; // length
typedef K<FLOAT> T; // temperature
typedef u<FLOAT> m; // mass
typedef angstrom_div_ps<FLOAT> v; // velocity
typedef angstrom_div_ps2<FLOAT> a; // acceleration
typedef u_mul_angstrom_div_ps2<FLOAT> f; // force
typedef u_mul_angstrom2_div_ps2<FLOAT> e; // energy
typedef ps<FLOAT> t; // time
// Declarations
auto mass = m(39.948);
auto temp = T(100);
auto epsilon = T(119.8);
auto dx = x(5.26);
auto sigma = x(3.405);
auto dt = t(0.01);
auto t_end = t(10);
auto N = ARRAYLIST(size_t, 4, 4, 4);
string molecule[4];
molecule[0] = "Ar";
molecule[1] = "Ar";
molecule[2] = "Ar";
molecule[3] = "Ar";
ofstream time_file;
time_file.open("time.dat");
auto t0 = clock();
// Boltzmann velocity dirstribution
Boltzmann<FLOAT> boltz(temp, mass);
Gaussian<v> gauss(boltz.StandardDeviation());
auto boltz_vel = delegate(gauss, &Gaussian<v>::Distribution_mu_0);
// Models
typedef VMD<x,Vector<v,3>> pos;
typedef VMD_Vel<x,v> vel;
typedef Vector<a,3> va;
typedef Array<va> acc;
typedef PBC<pos,vel,acc,void,x,3>::CX pref;
typedef PBC<pos,vel,acc,void,x,3>::CA aref;
typedef LJ_Potential<3,x,a,m,f,e> Potential;
typedef Delegate<void,pref&,aref&> LJ_Solver;
typedef PBC<pos,vel,acc,LJ_Solver,x,3> Boundary;
typedef Delegate<void,pos&> PeriodicBoundary;
typedef Delegate<void,pos&,vel&,acc&> List;
typedef VelocityVerlet<2,pos,vel,va,List> VerletModel;
typedef Delegate<void,t&> VerletSolver;
// Molecular dynamic model
MD_Model<m,t,x,v,VerletSolver,PeriodicBoundary> model(mass, dt, "Argon centered cubic lattice");
// Lennard-Jones potenial
Potential potential(sigma, mass, 0);
auto LJ_acc = delegate(potential, &Potential::Acceleration<pref,aref>);
// Periodic bounary condition
Boundary pbc(LJ_acc);
for(size_t i = 0; i < 3; i++) {
pbc.origin[i] = -0.25*dx;
pbc.range[i] = dx*(N[i]-0.25);
}
auto periodic_boundary = delegate(pbc, &Boundary::Boundary<pos>);
model.boundary = &periodic_boundary;
auto list = delegate(pbc, &Boundary::NeighbourList);
auto dist_vec = delegate(static_cast<MinImage<x,3>&>(pbc), &MinImage<x,3>::Distance<x,x>);
auto dist = delegate(&Euclidean::Length<Vector<x,3>>);
auto unit_vec = delegate(&Euclidean::UnitVector<x,x,3>);
potential.dist_vec = &dist_vec;
potential.dist = &dist;
potential.unit_vec = &unit_vec;
// Verlet differential solver
VerletModel verlet(static_cast<pos&>(model), static_cast<vel&>(model), list);
auto verlet_solver = delegate(verlet, &VerletModel::Solve<t>);
model.step = &verlet_solver;
// Lattice configuration
model.LatticeCenteredCubic(molecule, dx, N);
model.SetVelocityDistribution(boltz_vel);
auto data = static_cast<vel>(model);
TimeStep<t,decltype(model)> time(model);
// Task a and b
/*time.Open("b.xyz");
time.Print();
time.Close();*/
// Task c
auto step = delegate(model, &decltype(model)::Step<t,decltype(model)>);
auto Time = time;
/*Time.Open("c.xyz");
Run(Time, t_end, step);
Time.Close();*/
// Task d
auto boundary = delegate(model, &decltype(model)::Boundary<t,decltype(model)>);
/**time.data = data;
Time = time;
Time.Open("d.xyz");
Run(Time, t_end, step, boundary);
Time.Close();*/
// Task g
potential = epsilon * Boltzmann<FLOAT>::kB;
/**time.data = data;
Time = time;
Time.Open("g.xyz");
verlet = 0; // Initialize verlet solver
t0 = clock();
Run(Time, t_end, step, boundary);
time_file << (double)(clock()-t0)/CLOCKS_PER_SEC << " & ";
Time.Close();*/
// Task h
for(size_t i = 0; i < 3; i++)
pbc[i] = (pbc.range[i]-pbc.origin[i])/(3*sigma);
*time.data = data;
Time = time;
Time.Open("h.xyz");
verlet = 0; // Initialize verlet solver
t0 = clock();
Run(Time, t_end, step, boundary);
time_file << (double)(clock()-t0)/CLOCKS_PER_SEC << " \\\\ ";
Time.Close();
time_file.close();
return 0;
}
void Bubble:: upgrade_topology()
{
assert(size>=3);
assert(root!=NULL);
//--------------------------------------------------------------------------
// pass 0: pbc on vertices
//--------------------------------------------------------------------------
Tracer *p = root;
for( size_t i=size;i>0;--i,p=p->next)
{
pbc(p->vertex);
}
//--------------------------------------------------------------------------
// pass : refinement
//--------------------------------------------------------------------------
assert(root==p);
Tracer *q = p->next;
for( size_t i=0; i < size; ++i )
{
for(;;)
{
//------------------------------------------------------------------
// compute length to next vertex, with pbc
//------------------------------------------------------------------
Vertex pq(p->vertex,q->vertex);
pbc(pq);
p->s2 = pq.norm2(); assert(p->s2>0);
p->s = Sqrt( p->s2 );
//------------------------------------------------------------------
// do we refine ?
//------------------------------------------------------------------
if( p->s > lambda )
{
Tracer *I = cache.provide();
I->vertex.x = p->vertex.x + 0.5 * pq.x;
I->vertex.y = p->vertex.y + 0.5 * pq.y;
pbc(I->vertex);
insert_after(p, I);
assert(p->next==I);
assert(I->prev==p);
q = I;
continue;
}
//------------------------------------------------------------------
// ok, keep that in mind...
//------------------------------------------------------------------
p->edge= pq;
assert(p->s2>0);
assert(p->s>0);
break;
}
//----------------------------------------------------------------------
// next edge
//----------------------------------------------------------------------
p = q;
q = q->next;
}
}
/* build and update cell list */
static void updcells(mdsys_t *sys)
{
int i, ngrid, ncell, npair, midx, natoms;
double delta, boxby2, boxoffs;
boxby2 = 0.5 * sys->box;
natoms = sys->natoms;
if (sys->clist == NULL) {
int nidx;
ngrid = floor(cellrat * sys->box / sys->rcut);
ncell = ngrid*ngrid*ngrid;
delta = sys->box / ngrid;
boxoffs= boxby2 - 0.5*delta;
sys->delta = delta;
sys->ngrid = ngrid;
sys->ncell = ncell;
/* allocate cell list storage */
sys->clist = (cell_t *) malloc(ncell*sizeof(cell_t));
sys->plist = (int *) malloc(2*ncell*ncell*sizeof(int));
/* allocate index lists within cell. cell density < 2x avg. density */
nidx = 2*natoms / ncell + 2;
nidx = ((nidx/2) + 1) * 2;
sys->nidx = nidx;
for (i=0; i<ncell; ++i) {
sys->clist[i].idxlist = (int *) malloc(nidx*sizeof(int));
}
/* build cell pair list, assuming newtons 3rd law. */
npair = 0;
for (i=0; i < ncell-1; ++i) {
int j,k;
double x1,y1,z1;
k = i/ngrid/ngrid;
x1 = k*delta - boxoffs;
y1 = ((i-(k*ngrid*ngrid))/ngrid)*delta - boxoffs;
z1 = (i % ngrid)*delta - boxoffs;
for (j=i+1; j<ncell; ++j) {
double x2,y2,z2,rx,ry,rz;
k = j/ngrid/ngrid;
x2 = k*delta - boxoffs;
y2 = ((j-(k*ngrid*ngrid))/ngrid)*delta - boxoffs;
z2 = (j % ngrid)*delta - boxoffs;
rx=pbc(x1 - x2, boxby2, sys->box);
ry=pbc(y1 - y2, boxby2, sys->box);
rz=pbc(z1 - z2, boxby2, sys->box);
/* check for cells on a line that are too far apart */
if (fabs(rx) > sys->rcut+delta) continue;
if (fabs(ry) > sys->rcut+delta) continue;
if (fabs(rz) > sys->rcut+delta) continue;
/* check for cells in a plane that are too far apart */
if (sqrt(rx*rx+ry*ry) > (sys->rcut+sqrt(2.0)*delta)) continue;
if (sqrt(rx*rx+rz*rz) > (sys->rcut+sqrt(2.0)*delta)) continue;
if (sqrt(ry*ry+rz*rz) > (sys->rcut+sqrt(2.0)*delta)) continue;
/* other cells that are too far apart */
if (sqrt(rx*rx + ry*ry + rz*rz) > (sqrt(3.0)*delta+sys->rcut)) continue;
/* cells are close enough. add to list */
sys->plist[2*npair ] = i;
sys->plist[2*npair+1] = j;
++npair;
}
}
sys->npair = npair;
printf("Cell list has %dx%dx%d=%d cells with %d/%d pairs and "
"%d atoms/celllist.\n", ngrid, ngrid, ngrid, sys->ncell,
sys->npair, ncell*(ncell-1)/2, nidx);
}
/* reset cell list and sort atoms into cells */
ncell=sys->ncell;
delta=sys->delta;
ngrid=sys->ngrid;
for (i=0; i < sys->ncell; ++i) {
sys->clist[i].natoms=0;
}
boxoffs= boxby2 - 0.5*delta;
midx=0;
for (i=0; i < natoms; ++i) {
int idx,j,k,m,n;
k=floor((pbc(sys->pos[i], boxby2, sys->box)+boxby2)/delta);
m=floor((pbc(sys->pos[natoms + i], boxby2, sys->box)+boxby2)/delta);
n=floor((pbc(sys->pos[2*natoms + i], boxby2, sys->box)+boxby2)/delta);
j = ngrid*ngrid*k+ngrid*m+n;
idx = sys->clist[j].natoms;
sys->clist[j].idxlist[idx]=i;
++idx;
sys->clist[j].natoms = idx;
if (idx > midx) midx=idx;
}
if (midx > sys->nidx) {
printf("overflow in cell list: %d/%d atoms/cells.\n", midx, sys->nidx);
exit(1);
}
return;
}
void Pair_LJ::ComputeForce(Atoms *atom)
{
double epot;
#if defined(_OPENMP)
#pragma omp parallel reduction(+:epot)
#endif
{
double c12,c6,boxby2,rcsq;
double *fx, *fy, *fz;
double *rx, *ry, *rz;
int i, tid, fromidx, toidx, natoms, nthreads;
/* precompute some constants */
c12 = 4.0*epsilon*pow(sigma,12.0);
c6 = 4.0*epsilon*pow(sigma, 6.0);
rcsq= atom->GetRadCut() * atom->GetRadCut();
boxby2 = 0.5*atom->GetBoxSize();
natoms = atom->GetNAtoms();
epot = 0.0;
/* let each thread operate on a different
part of the enlarged force array */
#if defined(_OPENMP)
nthreads=omp_get_num_threads();
tid=omp_get_thread_num();
#else
nthreads=1;
tid=0;
#endif
fx=atom->GetForce() + (3*tid*natoms);
azzero(fx,3*natoms);
fy=atom->GetForce() + ((3*tid+1)*natoms);
fz=atom->GetForce() + ((3*tid+2)*natoms);
rx=atom->GetPosition();
ry=atom->GetPosition() + natoms;
rz=atom->GetPosition() + 2*natoms;
int x;
/* self interaction of atoms in cell */
for(i=0; i < atom->GetNCells(); i += nthreads) {
int j;
// cell_t *c1;
j = x = i + tid;
if (j >= (atom->GetNCells())) break;
// c1=atom->clist + j;
// afc=getlist(j)
for (j=0; j < atom->GetCellNAtoms(x)-1; ++j) {
// for (j=0; j < GetCellData()-1; ++j) {
int ii,k;
double rx1, ry1, rz1;
// ii=c1->idxlist[j];
ii=atom->GetCellIndex(x,j);
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=j+1; k < atom->GetCellNAtoms(x); ++k) {
int jj;
double rx2,ry2,rz2,rsq;
jj=atom->GetCellIndex(x,k);
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, atom->GetBoxSize());
ry2=pbc(ry1 - ry[jj], boxby2, atom->GetBoxSize());
rz2=pbc(rz1 - rz[jj], boxby2, atom->GetBoxSize());
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* interaction of atoms in different cells */
for(i=0; i < atom->GetNPairs(); i += nthreads) {
int j;
// const cell_t *c1, *c2;
j = x = i + tid;
if (x >= (atom->GetNPairs())) break;
// c1=atom->clist + atom->plist[2*x];
// c2=atom->clist + atom->plist[2*x+1];
for (j=0; j < atom->GetCellNAtoms(atom->GetPairItem(2*x)); ++j) {
int ii, k;
double rx1, ry1, rz1;
ii=atom->GetCellIndex(atom->GetPairItem(2*x),j);
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=0; k < atom->GetCellNAtoms(atom->GetPairItem(2*x+1)); ++k) {
int jj;
double rx2,ry2,rz2,rsq;
// jj=c2->idxlist[k];
jj = atom->GetCellIndex(atom->GetPairItem(2*x+1),k);
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, atom->GetBoxSize());
ry2=pbc(ry1 - ry[jj], boxby2, atom->GetBoxSize());
rz2=pbc(rz1 - rz[jj], boxby2, atom->GetBoxSize());
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* before reducing the forces, we have to make sure
that all threads are done adding to them. */
#if defined (_OPENMP)
#pragma omp barrier
#endif
/* set equal chunks of index ranges */
i = 1 + (3*natoms / nthreads);
fromidx = tid * i;
toidx = fromidx + i;
if (toidx > 3*natoms) toidx = 3*natoms;
/* reduce forces from threads with tid != 0 into
the storage of the first thread. since we have
threads already spawned, we do this in parallel. */
for (i=1; i < nthreads; ++i) {
int offs, j;
offs = 3*i*natoms;
for (j=fromidx; j < toidx; ++j) {
// atom->frc[j] += atom->frc[offs+j];
atom->SetForce(j,atom->GetForce(j)+atom->GetForce(offs+j));
}
}
}
atom->SetPotEnergy(epot);
}
/* compute LJ forces */
void force_LJ(mdsys_t *sys)
{
double pot;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i;
int natoms=sys->natoms;
/* zero energy and forces */
pot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
#pragma omp parallel for default(shared) private(i) reduction(+:pot)
for(i = 0; i < (natoms - 1); ++i) {
/* private versions of sys->rx[i] */
int j;
double rxi,ryi,rzi;
rxi = sys->rx[i];
ryi = sys->ry[i];
rzi = sys->rz[i];
for(j = (1 + i); j < natoms; ++j) {
double rx,ry,rz,rsq;
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(rxi - sys->rx[j], b);
ry=pbc(ryi - sys->ry[j], b);
rz=pbc(rzi - sys->rz[j], b);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
double rsqinv = 1/rsq;
double r6 = rsqinv*rsqinv*rsqinv;
double pr = p*r6;
double p6 = 4.0*sys->epsilon*pr;
double p12 = p6*pr;
double ffac;
ffac = rsqinv*(12*p12-6*p6);
pot += 0.5*(p12-p6);
#pragma omp atomic
sys->fx[i] += rx*ffac;
#pragma omp atomic
sys->fy[i] += ry*ffac;
#pragma omp atomic
sys->fz[i] += rz*ffac;
#pragma omp atomic
sys->fx[j] -= rx*ffac;
#pragma omp atomic
sys->fy[j] -= ry*ffac;
#pragma omp atomic
sys->fz[j] -= rz*ffac;
}
}
}
sys->epot = pot;
}
/* compute MORSE forces */
void force_morse(mdsys_t *sys)
{
double pot;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i;
int natoms=sys->natoms;
/* zero energy and forces */
pot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
#pragma omp parallel for default(shared) private(i) reduction(+:pot)
for(i = 0; i < (natoms - 1); ++i) {
/* private versions of sys->rx[i] */
int j;
double rxi,ryi,rzi;
rxi = sys->rx[i];
ryi = sys->ry[i];
rzi = sys->rz[i];
for(j = (1 + i); j < natoms; ++j) {
double rx,ry,rz,rsq;
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(rxi - sys->rx[j], b);
ry=pbc(ryi - sys->ry[j], b);
rz=pbc(rzi - sys->rz[j], b);
rs = sqrt(rsqi);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
esp = exp((-1)*sys->a*(rs-sys->rzero));
espq = exp((-1)*sys->a*(rs-sys->rzero)*(rs-sys->rzero));
ffac = 2*sys->De * (1-esp)*sys->a*esp;
pot += sys->De*(1-espq)
sys->fx[i] += rx*ffac;
#pragma omp atomic
sys->fy[i] += ry*ffac;
#pragma omp atomic
sys->fz[i] += rz*ffac;
#pragma omp atomic
sys->fx[j] -= rx*ffac;
#pragma omp atomic
sys->fy[j] -= ry*ffac;
#pragma omp atomic
sys->fz[j] -= rz*ffac;
}
}
}
sys->epot = pot;
}
bool ECPotentialBuilder::put(xmlNodePtr cur) {
if(localPot.empty()) {
int ng(IonConfig.getSpeciesSet().getTotalNum());
localZeff.resize(ng,1);
localPot.resize(ng,0);
nonLocalPot.resize(ng,0);
}
string ecpFormat("table");
string pbc("yes");
string forces("no");
OhmmsAttributeSet pAttrib;
pAttrib.add(ecpFormat,"format");
pAttrib.add(pbc,"pbc");
pAttrib.add(forces,"forces");
pAttrib.put(cur);
bool doForces = (forces == "yes") || (forces == "true");
//const xmlChar* t=xmlGetProp(cur,(const xmlChar*)"format");
//if(t != NULL) {
// ecpFormat= (const char*)t;
//}
if(ecpFormat == "xml")
{
useXmlFormat(cur);
}
else
{
useSimpleTableFormat();
}
///create LocalECPotential
bool usePBC =
!(IonConfig.Lattice.SuperCellEnum == SUPERCELL_OPEN || pbc =="no");
if(hasLocalPot) {
if(IonConfig.Lattice.SuperCellEnum == SUPERCELL_OPEN || pbc =="no")
{
#ifdef QMC_CUDA
LocalECPotential_CUDA* apot =
new LocalECPotential_CUDA(IonConfig,targetPtcl);
#else
LocalECPotential* apot = new LocalECPotential(IonConfig,targetPtcl);
#endif
for(int i=0; i<localPot.size(); i++) {
if(localPot[i]) apot->add(i,localPot[i],localZeff[i]);
}
targetH.addOperator(apot,"LocalECP");
}
else
{
if (doForces)
app_log() << " Will compute forces in CoulombPBCABTemp.\n" << endl;
#ifdef QMC_CUDA
CoulombPBCAB_CUDA* apot=
new CoulombPBCAB_CUDA(IonConfig,targetPtcl, doForces);
#else
CoulombPBCABTemp* apot =
new CoulombPBCABTemp(IonConfig,targetPtcl, doForces);
#endif
for(int i=0; i<localPot.size(); i++) {
if(localPot[i]) apot->add(i,localPot[i]);
}
targetH.addOperator(apot,"LocalECP");
}
//if(IonConfig.Lattice.BoxBConds[0]) {
// CoulombPBCABTemp* apot=new CoulombPBCABTemp(IonConfig,targetPtcl);
// for(int i=0; i<localPot.size(); i++) {
// if(localPot[i]) apot->add(i,localPot[i]);
// }
// targetH.addOperator(apot,"LocalECP");
//} else {
// LocalECPotential* apot = new LocalECPotential(IonConfig,targetPtcl);
// for(int i=0; i<localPot.size(); i++) {
// if(localPot[i]) apot->add(i,localPot[i],localZeff[i]);
// }
// targetH.addOperator(apot,"LocalECP");
//}
}
if(hasNonLocalPot) {
//resize the sphere
targetPtcl.resizeSphere(IonConfig.getTotalNum());
RealType rc2=0.0;
#ifdef QMC_CUDA
NonLocalECPotential_CUDA* apot =
new NonLocalECPotential_CUDA(IonConfig,targetPtcl,targetPsi,usePBC,doForces);
#else
NonLocalECPotential* apot =
new NonLocalECPotential(IonConfig,targetPtcl,targetPsi, doForces);
#endif
for(int i=0; i<nonLocalPot.size(); i++)
{
if(nonLocalPot[i])
{
rc2=std::max(rc2,nonLocalPot[i]->Rmax);
apot->add(i,nonLocalPot[i]);
}
}
targetPtcl.checkBoundBox(2*rc2);
targetH.addOperator(apot,"NonLocalECP");
for(int ic=0; ic<IonConfig.getTotalNum(); ic++)
{
int ig=IonConfig.GroupID[ic];
if(nonLocalPot[ig]) {
if(nonLocalPot[ig]->nknot) targetPtcl.Sphere[ic]->resize(nonLocalPot[ig]->nknot);
}
}
}
return true;
}
int main(int argc, char **argv)
{
PetscInitialize(&argc,&argv,PETSC_NULL,PETSC_NULL);
//PetscInitializeNoArguments();
//double bubbleDiam = 3.0E-3; // sqrt(Ar) = 535.83 ; Eo = 1.2091
//double bubbleDiam = 4.0E-3; // sqrt(Ar) = 824.96 ; Eo = 2.1495
double bubbleDiam = 5.2E-3; // sqrt(Ar) = 12228.0 ; Eo = 3.6327
double mu_in = 18.21E-6;
double mu_out = 958.08E-6;
double rho_in = 1.205;
double rho_out = 998.0;
double gravity = 9.8;
double sigma = 0.0728;
double betaGrad = 1.0; // 0.9625
double Re = sqrt( CalcArchimedesBuoyancy(gravity,bubbleDiam,rho_out,mu_out ) );
double We = CalcEotvos(gravity,bubbleDiam,rho_out,sigma);
double Fr = 1.0;
/*
// Rabello's thesis: sugar-syrup 1
double Re = 33.0413;
double Sc = 1.0;
double Fr = 1.0;
double We = 115.662;
double mu_in = 1.78E-5;
double mu_out = 0.5396;
double rho_in = 1.225;
double rho_out = 1350.0;
*/
int iter = 0;
double alpha = 1.0;
double cfl = 0.5;
double c1 = 0.0; // lagrangian
double c2 = 0.1; // smooth vel
double c3 = 10.0; // smooth coord (fujiwara)
double d1 = 1.0; // surface tangent velocity u_n=u-u_t
double d2 = 0.1; // surface smooth cord (fujiwara)
//const char* _frame = "fixed";
const char* _frame = "moving";
string physGroup = "\"wallInflowZeroU\"";
Solver *solverP = new PetscSolver(KSPGMRES,PCILU);
Solver *solverV = new PetscSolver(KSPCG,PCICC);
Solver *solverC = new PetscSolver(KSPCG,PCICC);
/*
string meshFile = "rising-moving-x.msh";
const char *binFolder = "/home/gcpoliveira/post-processing/vtk/3d/rising-pbc-moving/bin/";
const char *mshFolder = "/home/gcpoliveira/post-processing/vtk/3d/rising-pbc-moving/msh/";
const char *datFolder = "/home/gcpoliveira/post-processing/vtk/3d/rising-pbc-moving/dat/";
const char *vtkFolder = "/home/gcpoliveira/post-processing/vtk/3d/rising-pbc-moving/";
*/
// cell-2D
string meshFile = "unit-cell-s-2D-3d.msh";
// 1
/*
const char *binFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1/bin/";
const char *datFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1/dat/";
const char *mshFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1/msh/";
const char *vtkFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1/vtk/";
*/
// 2
/*
const char *binFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-2/bin/";
const char *datFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-2/dat/";
const char *mshFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-2/msh/";
const char *vtkFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-2/vtk/";
*/
// 3
const char *binFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-3/bin/";
const char *datFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-3/dat/";
const char *mshFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-3/msh/";
const char *vtkFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-2D-nb1-3/vtk/";
/*
// cell-D
string meshFile = "unit-cell-s-D-3d.msh";
const char *binFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-D-nb1/bin/";
const char *vtkFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-D-nb1/";
const char *datFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-D-nb1/dat/";
const char *mshFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-D-nb1/msh/";
*/
/*
// cell-0.5D
string meshFile = "unit-cell-s-0.5D-3d.msh";
const char *binFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-0.5D-nb1/bin/";
const char *vtkFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-0.5D-nb1/";
const char *datFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-0.5D-nb1/dat/";
const char *mshFolder = "/home/gcpoliveira/post-processing/vtk/3d/unit-cell-s-0.5D-nb1/msh/";
*/
string meshDir = (string) getenv("MESH3D_DIR");
if( strcmp( _frame,"moving") == 0 )
meshDir += "/rising/movingFrame/" + meshFile;
else
meshDir += "/rising/" + meshFile;
const char *mesh = meshDir.c_str();
Model3D m1;
cout << endl;
cout << "--------------> STARTING FROM 0" << endl;
cout << endl;
const char *mesh1 = mesh;
m1.readMSH(mesh1);
m1.setInterfaceBC();
m1.setTriEdge();
m1.mesh2Dto3D();
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.setSurfaceConfig();
m1.setInitSurfaceVolume();
m1.setInitSurfaceArea();
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC();
Periodic3D pbc(m1);
pbc.MountPeriodicVectorsNew("print");
Simulator3D s1(pbc,m1);
s1.setRe(Re);
s1.setWe(We);
s1.setFr(Fr);
s1.setC1(c1);
s1.setC2(c2);
s1.setC3(c3);
s1.setD1(d1);
s1.setD2(d2);
s1.setAlpha(alpha);
s1.setMu(mu_in,mu_out);
s1.setRho(rho_in,rho_out);
s1.setCfl(cfl);
s1.init();
s1.setBetaPressureLiquid(betaGrad);
s1.setDtALETwoPhase();
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
// Point's distribution
Helmholtz3D h1(m1);
h1.setBC();
h1.initRisingBubble();
//h1.initThreeBubbles();
h1.assemble();
h1.setk(0.2);
h1.matMountC();
h1.setUnCoupledCBC();
h1.setCRHS();
h1.unCoupledC();
h1.setModel3DEdgeSize();
InOut save(m1,s1); // cria objeto de gravacao
save.saveVTK(vtkFolder,"geometry");
save.saveVTKSurface(vtkFolder,"geometry");
save.saveMeshInfo(datFolder);
save.saveInfo(datFolder,"info",mesh);
double vinst=0;
double vref=0;
double xref=0;
double xinit=0;
double dx=0;
if( strcmp( _frame,"moving") == 0 )
{
// moving
vref = s1.getURef();
xref = s1.getXRef();
s1.setCentroidVelPos();
xinit = s1.getCentroidPosXAverage();
}
int nIter = 30000;
int nReMesh = 1;
for( int i=1;i<=nIter;i++ )
{
for( int j=0;j<nReMesh;j++ )
{
cout << color(none,magenta,black);
cout << "____________________________________ Iteration: "
<< iter << endl << endl;
cout << resetColor();
// moving
if( strcmp( _frame,"moving") == 0 )
{
// moving frame
dx = s1.getCentroidPosXAverage() - xinit;
vinst = s1.getCentroidVelXAverage() + dx/s1.getDt();
vref += vinst;
xref += vref*s1.getDt();
cout << "vref: " << vref << " xref: " << xref << endl;
cout << "dx: " << dx << endl;
s1.setUSol(vinst);
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC(vref);
pbc.MountPeriodicVectorsNew("print");
s1.setURef(vref);
s1.setXRef(xref);
}
s1.setDtALETwoPhase();
InOut save(m1,s1); // cria objeto de gravacao
save.printSimulationReport();
s1.stepALEPBC();
s1.movePoints();
s1.assemble();
s1.matMount();
s1.setUnCoupledBC();
s1.setGravity("-X");
s1.setBetaFlowLiq("+X");
s1.setRHS();
s1.setCopyDirectionPBC("RL");
s1.setInterfaceGeo();
//s1.setInterfaceLevelSet();
s1.unCoupledPBCNew();
save.saveMSH(mshFolder,"newMesh",iter);
save.saveVTK(vtkFolder,"sim",iter);
save.saveVTKSurface(vtkFolder,"sim",iter);
save.saveSol(binFolder,"sim",iter);
save.saveBubbleInfo(datFolder);
//save.crossSectionalVoidFraction(datFolder,"voidFraction",iter);
save.saveBubbleShapeFactors(datFolder,"shapeFactors",iter);
s1.saveOldData();
cout << color(none,magenta,black);
cout << "________________________________________ END of "
<< iter << endl << endl;;
cout << resetColor();
s1.timeStep();
iter++;
}
Helmholtz3D h2(m1,h1);
h2.setBC();
h2.initRisingBubble();
//h2.initThreeBubbles();
h2.assemble();
h2.matMountC();
h2.setUnCoupledCBC();
h2.setCRHS();
h2.unCoupledC();
h2.setModel3DEdgeSize();
Model3D mOld = m1;
/* *********** MESH TREATMENT ************* */
// set normal and kappa values
m1.setNormalAndKappa();
m1.initMeshParameters();
// 3D operations
m1.insert3dMeshPointsByDiffusion(6.0);
m1.remove3dMeshPointsByDiffusion(1.0);
//m1.removePointByVolume();
//m1.removePointsByInterfaceDistance();
//m1.remove3dMeshPointsByDistance();
m1.remove3dMeshPointsByHeight();
m1.delete3DPoints();
// surface operations
m1.smoothPointsByCurvature();
m1.insertPointsByLength("curvature");
//m1.insertPointsByCurvature("flat");
//m1.removePointsByCurvature();
//m1.insertPointsByInterfaceDistance("flat");
m1.contractEdgesByLength("curvature");
//m1.removePointsByLength();
m1.flipTriangleEdges();
m1.removePointsByNeighbourCheck();
//m1.checkAngleBetweenPlanes();
/* **************************************** */
//m1.mesh2Dto3DOriginal();
m1.mesh3DPoints();
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.setSurfaceConfig();
if( strcmp( _frame,"moving") == 0 )
{
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC(vref);
pbc.MountPeriodicVectorsNew("print");
}
else
{
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC();
pbc.MountPeriodicVectorsNew("noPrint");
}
Simulator3D s2(m1,s1);
s2.applyLinearInterpolation(mOld);
s1 = s2;
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
InOut saveEnd(m1,s1); // cria objeto de gravacao
saveEnd.printMeshReport();
saveEnd.saveMeshInfo(datFolder);
}
PetscFinalize();
return 0;
}
int main(){
bool deposit = true;
printf("Enter value for diffusion rate D: ");
scanf(" %f", &D);
printf("Enter value for deposition rate F: ");
scanf(" %f", &F);
printf("Enter total number of steps: ");
scanf(" %d", &steps);
FILE *file = fopen("Output.txt", "w");
fclose(file);
int deposition_ct=0;
create_lattice();
//sets inverse pointer array to -1
for(i=0;i<L;i++){
for(j=0;j<L;j++){
ipointa[i][j]=-1;
}}
//initialize ip and im arrays to take care to pbc's easilyn
for(i=0;i<L;i++){
ip[i]=i+1;
im[i]=i-1;
}
ip[L-1]=0;
im[0]=L-1;
//initialize nbxa[L][4] and nbya[L][4] for the 4 directions
for(i=0;i<L;i++){
nbxa[i][0]=ip[i];
nbya[i][0]=i;
nbxa[i][1]=i;
nbya[i][1]=im[i];
nbxa[i][2]=im[i];
nbya[i][2]=i;
nbxa[i][3]=i;
nbya[i][3]=ip[i];
}
for(int i = 0; i <steps; i++){
float Rdep = F*(L^2);
float Rdiff = monomer_ct * D;
P_d = Rdep / (Rdep + Rdiff);
P_f = 1 - P_d;
float random = (rand() % 10000)/10000.0;
fprintf(debug, "P_d %f, random %f\n", P_d, random);
fprintf(debug, "monomer_ct %d\n", monomer_ct);
if((random < P_d) /*&& (deposit)*/){
deposition();
fprintf(debug, "Deposition \n");
deposition_ct++;
}
else{
fprintf(debug, "Carrying out diffusion\n");
diffusion();
//printf("Diffusion \n");
}
pbc();
print_walkers();
output();
//draw();
}
}
int main(int argc, char **argv)
{
PetscInitialize(&argc,&argv,PETSC_NULL,PETSC_NULL);
//PetscInitializeNoArguments();
int iter = 0;
double velVCrossflow = 0.0; // i.e. V_crossflow = velVCrossflow x V_jet
double velWCrossflow = velVCrossflow;
//const char* _frame = "fixed";
const char* _frame = "moving";
string _physGroup = "\"wallInflowVTransverse\"";
double betaGrad = 0.0;
Solver *solverP = new PetscSolver(KSPCG,PCILU);
Solver *solverV = new PCGSolver();
Solver *solverC = new PCGSolver();
string meshFile = "crossflow-3d-Lp1.5-b0.09.msh";
const char* name = "ms";
const char *binFolder = "null";
const char *datFolder = "null";
const char *mshFolder = "null";
const char *vtkFolder = "null";
if( strcmp( name,"wl") == 0 )
{
binFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/bin/";
datFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/dat/";
mshFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/msh/";
vtkFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/vtk/";
}
else
{
binFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/bin/";
datFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/dat/";
mshFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/msh/";
vtkFolder = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/vtk/";
}
string meshDir = (string) getenv("MESH3D_DIR");
if( strcmp( _frame,"moving") == 0 )
meshDir += "/rising/movingFrame/" + meshFile;
else
meshDir += "/rising/" + meshFile;
const char *mesh = meshDir.c_str();
Model3D m1;
cout << endl;
cout << "--------------> RE-STARTING..." << endl;
cout << endl;
string mshBase = "null";
if( strcmp( name,"wl") == 0 )
mshBase = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/msh/newMesh-";
else
mshBase = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/msh/newMesh-";
// load surface mesh
string aux = *(argv+1);
string file = mshBase + *(argv+1) + (string) ".msh";
const char *mesh2 = file.c_str();
m1.readMSH(mesh2);
m1.setInterfaceBC();
m1.setTriEdge();
m1.mesh2Dto3D();
string vtkBase = "null";
if( strcmp( name,"wl") == 0 )
vtkBase = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/vtk/sim-";
else
vtkBase = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/vtk/sim-";
// load 3D mesh
file = vtkBase + *(argv+1) + (string) ".vtk";
const char *vtkFile = file.c_str();
m1.readVTK(vtkFile);
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.readVTKHeaviside(vtkFile);
m1.setSurfaceConfig();
m1.setInitSurfaceVolume();
m1.setInitSurfaceArea();
m1.setCrossflowVVelocity(velVCrossflow);
m1.setCrossflowWVelocity(velWCrossflow);
m1.setGenericBCPBCNew(_physGroup);
m1.setGenericBC();
Periodic3D pbc(m1);
//pbc.MountPeriodicVectorsNew("noPrint");
pbc.MountPeriodicVectors("noPrint");
Simulator3D s1(pbc,m1);
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
const char *dirBase = "null";
if( strcmp( name,"wl") == 0 )
dirBase = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-1.0-longmire-Lp5/";
else
dirBase = "/work/gcpoliveira/post-processing/3d/crossflow-lambda-0.0-meister-Lp1.5-b0.09/";
iter = s1.loadSolution(dirBase,"sim",atoi(*(argv+1)));
// Point's distribution
Helmholtz3D h1(m1);
h1.setBC();
h1.initRisingBubble();
h1.assemble();
h1.setk(0.2);
h1.matMountC();
h1.setUnCoupledCBC();
h1.setCRHS();
h1.unCoupledC();
h1.setModel3DEdgeSize();
InOut save(m1,s1); // cria objeto de gravacao
save.saveVTKSurface(vtkFolder,"geometry");
save.saveVTKPBC(vtkFolder,"initial",0,betaGrad);
save.saveMeshInfo(datFolder);
save.saveInfo(datFolder,"info",mesh);
double uinst=0;
double vinst=0;
double winst=0;
double uref=0;
double vref=0;
double wref=0;
double xref=0;
double yref=0;
double zref=0;
double xinit=0;
double yinit=0;
double zinit=0;
double dx=0;
double dy=0;
double dz=0;
if( strcmp( _frame,"moving") == 0 )
{
// moving
uref = s1.getURef();
xref = s1.getXRef();
vref = s1.getVRef();
yref = s1.getYRef();
wref = s1.getWRef();
zref = s1.getZRef();
s1.setCentroidVelPos();
xinit = s1.getCentroidPosXAverage(); // initial x centroid
yinit = s1.getCentroidPosYAverage(); // initial y centroid
zinit = s1.getCentroidPosZAverage(); // initial z centroid
}
int nIter = 50000;
int nReMesh = 1;
for( int i=1;i<=nIter;i++ )
{
for( int j=0;j<nReMesh;j++ )
{
cout << color(none,magenta,black);
cout << "____________________________________ Iteration: "
<< iter << endl;
cout << resetColor();
if( strcmp( _frame,"moving") == 0 )
{
// moving frame
dx = s1.getCentroidPosXAverage() - xinit; // mov. frame x displacement
dy = s1.getCentroidPosYAverage() - yinit; // mov. frame y displacement
dz = s1.getCentroidPosZAverage() - zinit; // mov. frame z displacement
uinst = s1.getCentroidVelXAverage() + dx/s1.getDt(); // uc + correction
vinst = s1.getCentroidVelYAverage() + dy/s1.getDt(); // vc + correction
winst = s1.getCentroidVelZAverage() + dz/s1.getDt(); // wc + correction
uref += uinst; // sums to recover inertial vel
vref += vinst;
wref += winst;
xref += uref*s1.getDt();
yref += vref*s1.getDt();
zref += wref*s1.getDt();
cout << "uref: " << uref << " xref: " << xref << endl;
cout << "vref: " << vref << " yref: " << yref << endl;
cout << "wref: " << wref << " zref: " << zref << endl;
cout << "uinst: " << uinst << " vinst: " << vinst << " winst: " << winst << endl;
cout << "dx: " << dx << endl;
cout << "dy: " << dy << endl;
cout << "dz: " << dz << endl;
s1.setUSol(uinst); // subtraction for inertial frame: u - u_MFR
s1.setVSol(vinst); // subtraction for inertial frame: v - v_MFR
s1.setWSol(winst); // subtraction for inertial frame: w - w_MFR
m1.setCrossflowVVelocity(velVCrossflow); // set of crossflow velocity for BC
m1.setCrossflowWVelocity(velWCrossflow); // set of crossflow velocity for BC
m1.setGenericBCPBCNew(_physGroup);
m1.setGenericBC(uref,vref,wref); // crossflow condition
//pbc.MountPeriodicVectorsNew("print");
pbc.MountPeriodicVectors("print");
s1.setURef(uref); // sets to recover the inertial physics; ease prints in InOut
s1.setVRef(vref);
s1.setWRef(wref);
s1.setXRef(xref);
s1.setYRef(yref);
s1.setZRef(zref);
}
s1.setDtALETwoPhase();
InOut save(m1,s1); // cria objeto de gravacao
save.printSimulationReport();
s1.stepALEPBC();
s1.movePoints();
s1.assemble();
s1.matMount();
s1.setUnCoupledBC();
//s1.setGravity("-Z");
//s1.setBetaFlowLiq("+X");
s1.setRHS();
s1.setCopyDirectionPBC("RL");
s1.setInterfaceGeo();
//s1.unCoupledPBCNew();
s1.unCoupledPBC();
if ( i%15 == 0 )
{
save.saveVTKPBC(vtkFolder,"sim",iter,betaGrad);
save.saveVTKSurfacePBC(vtkFolder,"sim",iter,betaGrad);
save.saveMSH(mshFolder,"newMesh",iter);
save.saveSol(binFolder,"sim",iter);
save.saveBubbleInfo(datFolder);
save.bubbleWallDistance(datFolder,"dist",iter);
save.saveBubbleShapeFactors(datFolder,"shapeFactors",iter);
}
s1.saveOldData();
cout << color(none,magenta,black);
cout << "________________________________________ END of "
<< iter << endl;
cout << resetColor();
s1.timeStep();
iter++;
}
Helmholtz3D h2(m1,h1);
h2.setBC();
h2.initRisingBubble();
h2.assemble();
h2.setk(0.2);
h2.matMountC();
h2.setUnCoupledCBC();
h2.setCRHS();
h2.unCoupledC();
h2.saveVTK(vtkFolder,"edge",iter-1);
//h2.saveChordalEdge(datFolder,"edge",iter-1);
h2.setModel3DEdgeSize();
Model3D mOld = m1;
/* *********** MESH TREATMENT ************* */
m1.setNormalAndKappa();
m1.initMeshParameters();
// 3D mesh operations
m1.insert3dMeshPointsByDiffusion(6.5);
m1.remove3dMeshPointsByDiffusion(1.5);
//m1.removePointByVolume();
//m1.removePointsByInterfaceDistance();
//m1.remove3dMeshPointsByDistance();
m1.remove3dMeshPointsByHeight();
m1.delete3DPoints();
// surface mesh operations
m1.smoothPointsByCurvature();
m1.insertPointsByLength("curvature");
//m1.insertPointsByCurvature("flat");
//m1.removePointsByCurvature();
//m1.insertPointsByInterfaceDistance("flat");
m1.contractEdgesByLength("curvature");
//m1.removePointsByLength();
m1.flipTriangleEdges();
m1.removePointsByNeighbourCheck();
//m1.checkAngleBetweenPlanes();
/* **************************************** */
m1.mesh3DPoints();
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.setSurfaceConfig();
if( strcmp( _frame,"moving") == 0 )
{
m1.setCrossflowVVelocity(velVCrossflow);
m1.setCrossflowWVelocity(velWCrossflow);
m1.setGenericBCPBCNew(_physGroup);
m1.setGenericBC(uref,vref,wref);
//pbc.MountPeriodicVectorsNew("noPrint");
pbc.MountPeriodicVectors("noPrint");
}
else
{
m1.setCrossflowVVelocity(velVCrossflow);
m1.setCrossflowWVelocity(velWCrossflow);
m1.setGenericBCPBCNew(_physGroup);
m1.setGenericBC();
//pbc.MountPeriodicVectorsNew("noPrint");
pbc.MountPeriodicVectors("noPrint");
}
Simulator3D s2(m1,s1);
s2.applyLinearInterpolation(mOld);
s1 = s2;
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
if ( i%15 == 0 )
{
InOut saveEnd(m1,s1); // cria objeto de gravacao
saveEnd.printMeshReport();
saveEnd.saveMeshInfo(datFolder);
}
}
PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
PetscInitialize(&argc,&argv,PETSC_NULL,PETSC_NULL);
//PetscInitializeNoArguments();
// bogdan's thesis 2010 (Bhaga and Weber, JFM 1980)
int iter = 1;
double Re = 100;
double Sc = 1;
double We = 115.662;
double Fr = 1.0;
double alpha = 1.0;
double rho_in = 1.225;
double rho_out =1350;
double mu_out = 1;
double mu_in = 0.0000178;
const char* _case = "3";
// case 1
if( strcmp( _case,"1") == 0 )
{
Re = sqrt(42.895);
mu_out = 2.73;
}
else if( strcmp( _case,"2") == 0 )
{
Re = 13.8487; // case 2
mu_out = 1.28;
}
else if( strcmp( _case,"3") == 0 )
{
Re = 33.0413; // case 3
mu_out = 0.5396; // case 3
}
else if( strcmp( _case,"6") == 0 )
{
Re = sqrt(3892.856); // case 6
mu_out = 0.2857; // case 6
}
else if( strcmp( _case,"7") == 0 )
{
Re = sqrt(18124.092); // case 7
mu_out = 0.1324; // case 7
}
else if( strcmp( _case,"8") == 0 )
{
Re = sqrt(41505.729); // case 8 (extream)
mu_out = 0.0875134907735; // extream
}
else
{
cerr << "test case " << _case << " not available!" << endl;
exit(1);
}
double cfl = 0.1;
//string meshFile = "rising-x.msh";
string meshFile = "airWaterSugarPBC-wallLeftRight.msh";
string physGroup = "\"wallNoSlip\"";
double betaGrad = 1.0;
const char* _frame = "fixed";
//const char* _frame = "moving";
// fixed
double c1 = 0.0; // lagrangian
double c2 = 1.0; // smooth vel
double c3 = 10.0; // smooth coord (fujiwara)
double d1 = 1.0; // surface tangent vel = (u-ut)
double d2 = 0.2; // surface smooth coord (fujiwara)
// moving
if( strcmp( _frame,"moving") == 0 )
{
c1 = 0.0; // lagrangian
c2 = 1.0; // smooth vel: OBS - different result with c1=0.0
c3 = 10.0; // smooth coord (fujiwara)
d1 = 0.0; // surface tangent velocity u_n=u-u_t
d2 = 0.1; // surface smooth cord (fujiwara)
}
Solver *solverP = new PetscSolver(KSPCG,PCICC);
//Solver *solverP = new PetscSolver(KSPGMRES,PCILU);
//Solver *solverP = new PetscSolver(KSPGMRES,PCJACOBI);
Solver *solverV = new PetscSolver(KSPCG,PCICC);
//Solver *solverV = new PetscSolver(KSPCG,PCJACOBI);
Solver *solverC = new PetscSolver(KSPCG,PCICC);
const char *binFolder = "/work/gcpoliveira/post-processing/3d/risingPBC/bin/";
const char *vtkFolder = "/work/gcpoliveira/post-processing/3d/risingPBC/vtk/";
const char *datFolder = "/work/gcpoliveira/post-processing/3d/risingPBC/dat/";
const char *mshFolder = "/work/gcpoliveira/post-processing/3d/risingPBC/msh/";
string meshDir = (string) getenv("MESH3D_DIR");
if( strcmp( _frame,"moving") == 0 )
meshDir += "/twoPhase/pbc/" + meshFile;
else
meshDir += "/twoPhase/pbc/" + meshFile;
const char *mesh = meshDir.c_str();
Model3D m1;
cout << endl;
cout << "--------------> STARTING FROM 0" << endl;
cout << endl;
const char *mesh1 = mesh;
m1.readMSH(mesh1);
m1.setInterfaceBC();
m1.setTriEdge();
m1.mesh2Dto3D();
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.setSurfaceConfig();
m1.setInitSurfaceVolume();
m1.setInitSurfaceArea();
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC();
Periodic3D pbc(m1);
pbc.MountPeriodicVectorsNew("print");
Simulator3D s1(pbc,m1);
s1.setRe(Re);
s1.setSc(Sc);
s1.setWe(We);
s1.setFr(Fr);
s1.setC1(c1);
s1.setC2(c2);
s1.setC3(c3);
s1.setD1(d1);
s1.setD2(d2);
s1.setAlpha(alpha);
s1.setMu(mu_in,mu_out);
s1.setRho(rho_in,rho_out);
s1.setCfl(cfl);
s1.init();
s1.setBetaPressureLiquid(betaGrad);
s1.setDtALETwoPhase();
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
// Point's distribution
Helmholtz3D h1(m1);
h1.setBC();
h1.initRisingBubble();
h1.assemble();
h1.setk(0.2);
h1.matMountC();
h1.setUnCoupledCBC();
h1.setCRHS();
h1.unCoupledC();
h1.setModel3DEdgeSize();
InOut save(m1,s1); // cria objeto de gravacao
save.saveVTK(vtkFolder,"geometry");
save.saveVTKSurface(vtkFolder,"geometry");
save.saveMeshInfo(datFolder);
save.saveInfo(datFolder,"info",mesh);
double vinst=0;
double vref=0;
double xref=0;
double xinit=0;
double dx=0;
if( strcmp( _frame,"moving") == 0 )
{
// moving
xref = s1.getURef();
xref = s1.getXRef();
s1.setCentroidVelPos();
xinit = s1.getCentroidPosXAverage();
}
int nIter = 300;
int nReMesh = 1;
for( int i=1;i<=nIter;i++ )
{
for( int j=0;j<nReMesh;j++ )
{
cout << color(none,magenta,black);
cout << "____________________________________ Iteration: "
<< iter << endl << endl;
cout << resetColor();
// moving
if( strcmp( _frame,"moving") == 0 )
{
// moving frame
dx = s1.getCentroidPosXAverage() - xinit;
vinst = s1.getCentroidVelXAverage() + dx/s1.getDt();
vref += vinst;
xref += vref*s1.getDt();
cout << "vref: " << vref << " xref: " << xref << endl;
cout << "dx: " << dx << endl;
s1.setUSol(vinst);
m1.setGenericBC(vref);
s1.setURef(vref);
s1.setXRef(xref);
}
//s1.stepLagrangian();
s1.stepALEPBC();
s1.setDtALETwoPhase();
InOut save(m1,s1); // cria objeto de gravacao
save.printSimulationReport();
s1.movePoints();
s1.assemble();
s1.matMount();
s1.setUnCoupledBC();
s1.setGravity("-X");
s1.setBetaFlowLiq("+X");
s1.setRHS();
s1.setCopyDirectionPBC("RL");
s1.setInterfaceGeo();
s1.unCoupledPBCNew();
if ( i%5 == 0 )
{
save.saveMSH(mshFolder,"newMesh",iter);
save.saveVTK(vtkFolder,"sim",iter);
save.saveVTKSurface(vtkFolder,"sim",iter);
save.saveSol(binFolder,"sim",iter);
save.saveBubbleInfo(datFolder);
}
s1.saveOldData();
cout << color(none,magenta,black);
cout << "________________________________________ END of "
<< iter << endl << endl;;
cout << resetColor();
s1.timeStep();
iter++;
}
Helmholtz3D h2(m1,h1);
h2.setBC();
h2.initRisingBubble();
h2.assemble();
h2.setk(0.2);
h2.matMountC();
h2.setUnCoupledCBC();
h2.setCRHS();
h2.unCoupledC();
if ( i%5 == 0 )
{
h2.saveVTK(vtkFolder,"edge",iter-1);
h2.saveChordalEdge(datFolder,"edge",iter-1);
h2.setModel3DEdgeSize();
}
Model3D mOld = m1;
/* *********** MESH TREATMENT ************* */
// set normal and kappa values
m1.setNormalAndKappa();
m1.initMeshParameters();
// 3D operations
m1.insert3dMeshPointsByDiffusion(6.0);
m1.remove3dMeshPointsByDiffusion(0.5);
//m1.removePointByVolume();
//m1.removePointsByInterfaceDistance();
//m1.remove3dMeshPointsByDistance();
m1.remove3dMeshPointsByHeight();
m1.delete3DPoints();
// surface operations
m1.smoothPointsByCurvature();
m1.insertPointsByLength("flat");
//m1.insertPointsByCurvature("flat");
//m1.removePointsByCurvature();
//m1.insertPointsByInterfaceDistance("flat");
m1.contractEdgesByLength("flat");
//m1.removePointsByLength();
m1.flipTriangleEdges();
m1.removePointsByNeighbourCheck();
//m1.checkAngleBetweenPlanes();
/* **************************************** */
//m1.mesh2Dto3DOriginal();
m1.mesh3DPoints();
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.setSurfaceConfig();
if( strcmp( _frame,"moving") == 0 )
{
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC(vref);
pbc.MountPeriodicVectorsNew("noPrint");
}
else
{
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC();
pbc.MountPeriodicVectorsNew("noPrint");
}
Simulator3D s2(m1,s1);
s2.applyLinearInterpolation(mOld);
s1 = s2;
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
InOut saveEnd(m1,s1); // cria objeto de gravacao
saveEnd.printMeshReport();
saveEnd.saveMeshInfo(datFolder);
}
PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
PetscInitialize(&argc,&argv,PETSC_NULL,PETSC_NULL);
//PetscInitializeNoArguments();
int iter = 0;
//const char* _frame = "fixed";
const char* _frame = "moving";
string physGroup = "\"wallInflowZeroU\"";
//string physGroup = "\"wallNoSlip\"";
double betaGrad = 1.0;
Solver *solverP = new PetscSolver(KSPCG,PCICC);
Solver *solverV = new PetscSolver(KSPCG,PCICC);
Solver *solverC = new PetscSolver(KSPCG,PCICC);
// rising-pbc
//string meshFile = "airWaterSugarPBC-wallLeftRight.msh";
/*
const char *binFolder = "/work/gcpoliveira/post-processing/3d/rising-pbc/bin/";
const char *mshFolder = "/work/gcpoliveira/post-processing/3d/rising-pbc/msh/";
const char *datFolder = "/work/gcpoliveira/post-processing/3d/rising-pbc/dat/";
const char *vtkFolder = "/work/gcpoliveira/post-processing/3d/rising-pbc/vtk/";
*/
// rising-beta
/*
const char *binFolder = "/work/gcpoliveira/post-processing/3d/rising-beta/bin/";
const char *mshFolder = "/work/gcpoliveira/post-processing/3d/rising-beta/msh/";
const char *datFolder = "/work/gcpoliveira/post-processing/3d/rising-beta/dat/";
const char *vtkFolder = "/work/gcpoliveira/post-processing/3d/rising-beta/vtk/";
*/
// cell-2D
string meshFile = "unit-cell-s-2D-3d.msh";
// 1
/*
const char *binFolder = "/work/gcpoliveira/post-processing/3d/cell-1/bin/";
const char *datFolder = "/work/gcpoliveira/post-processing/3d/cell-1/dat/";
const char *mshFolder = "/work/gcpoliveira/post-processing/3d/cell-1/msh/";
const char *vtkFolder = "/work/gcpoliveira/post-processing/3d/cell-1/vtk/";
*/
// 2
/*
const char *binFolder = "/work/gcpoliveira/post-processing/3d/cell-2/bin/";
const char *datFolder = "/work/gcpoliveira/post-processing/3d/cell-2/dat/";
const char *mshFolder = "/work/gcpoliveira/post-processing/3d/cell-2/msh/";
const char *vtkFolder = "/work/gcpoliveira/post-processing/3d/cell-2/vtk/";
*/
// 3
const char *binFolder = "/work/gcpoliveira/post-processing/3d/cell-3/bin/";
const char *datFolder = "/work/gcpoliveira/post-processing/3d/cell-3/dat/";
const char *mshFolder = "/work/gcpoliveira/post-processing/3d/cell-3/msh/";
const char *vtkFolder = "/work/gcpoliveira/post-processing/3d/cell-3/vtk/";
string meshDir = (string) getenv("MESH3D_DIR");
if( strcmp( _frame,"moving") == 0 )
meshDir += "/rising/movingFrame/" + meshFile;
else
meshDir += "/rising/" + meshFile;
const char *mesh = meshDir.c_str();
Model3D m1;
cout << endl;
cout << "--------------> RE-STARTING..." << endl;
cout << endl;
//string mshBase = "/work/gcpoliveira/post-processing/3d/cell-1/msh/newMesh-";
//string mshBase = "/work/gcpoliveira/post-processing/3d/cell-2/msh/newMesh-";
string mshBase = "/work/gcpoliveira/post-processing/3d/cell-3/msh/newMesh-";
//string mshBase = "/work/gcpoliveira/post-processing/3d/rising-pbc/msh/newMesh-";
//string mshBase = "/work/gcpoliveira/post-processing/3d/rising-beta/msh/newMesh-";
// load surface mesh
string aux = *(argv+1);
string file = mshBase + *(argv+1) + (string) ".msh";
const char *mesh2 = file.c_str();
m1.readMSH(mesh2);
m1.setInterfaceBC();
m1.setTriEdge();
m1.mesh2Dto3D();
//string vtkBase = "/work/gcpoliveira/post-processing/3d/cell-1/vtk/sim-";
//string vtkBase = "/work/gcpoliveira/post-processing/3d/cell-2/vtk/sim-";
string vtkBase = "/work/gcpoliveira/post-processing/3d/cell-3/vtk/sim-";
//string vtkBase = "/work/gcpoliveira/post-processing/3d/rising-pbc/vtk/sim-";
//string vtkBase = "/work/gcpoliveira/post-processing/3d/rising-beta/vtk/sim-";
// load 3D mesh
file = vtkBase + *(argv+1) + (string) ".vtk";
const char *vtkFile = file.c_str();
m1.readVTK(vtkFile);
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.readVTKHeaviside(vtkFile);
m1.setSurfaceConfig();
m1.setInitSurfaceVolume();
m1.setInitSurfaceArea();
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC();
Periodic3D pbc(m1);
pbc.MountPeriodicVectorsNew("print");
Simulator3D s1(pbc,m1);
s1.setBetaPressureLiquid(betaGrad);
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
//const char *dirBase = "/work/gcpoliveira/post-processing/3d/cell-1/";
//const char *dirBase = "/work/gcpoliveira/post-processing/3d/cell-2/";
const char *dirBase = "/work/gcpoliveira/post-processing/3d/cell-3/";
//const char *dirBase = "/work/gcpoliveira/post-processing/3d/rising-pbc/";
//const char *dirBase = "/work/gcpoliveira/post-processing/3d/rising-beta/";
iter = s1.loadSolution(dirBase,"sim",atoi(*(argv+1)));
// Point's distribution
Helmholtz3D h1(m1);
h1.setBC();
h1.initRisingBubble();
//h1.initThreeBubbles();
h1.assemble();
h1.setk(0.2);
h1.matMountC();
h1.setUnCoupledCBC();
h1.setCRHS();
h1.unCoupledC();
h1.setModel3DEdgeSize();
InOut save(m1,s1); // cria objeto de gravacao
save.saveVTK(vtkFolder,"geometry");
save.saveVTKSurface(vtkFolder,"geometry");
save.saveMeshInfo(datFolder);
save.saveInfo(datFolder,"info",mesh);
double vinst=0;
double vref=0;
double xref=0;
double xinit=0;
double dx=0;
if( strcmp( _frame,"moving") == 0 )
{
// moving
vref = s1.getURef();
xref = s1.getXRef();
s1.setCentroidVelPos();
xinit = s1.getCentroidPosXAverage();
}
int nIter = 30000;
int nReMesh = 1;
for( int i=1;i<=nIter;i++ )
{
for( int j=0;j<nReMesh;j++ )
{
cout << color(none,magenta,black);
cout << "____________________________________ Iteration: "
<< iter << endl << endl;
cout << resetColor();
// moving
if( strcmp( _frame,"moving") == 0 )
{
// moving frame
dx = s1.getCentroidPosXAverage() - xinit;
vinst = s1.getCentroidVelXAverage() + dx/s1.getDt();
vref += vinst;
xref += vref*s1.getDt();
cout << "vref: " << vref << " xref: " << xref << endl;
cout << "dx: " << dx << endl;
s1.setUSol(vinst);
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC(vref);
pbc.MountPeriodicVectorsNew("print");
s1.setURef(vref);
s1.setXRef(xref);
}
s1.setDtALETwoPhase();
InOut save(m1,s1); // cria objeto de gravacao
save.printSimulationReport();
s1.stepALEPBC();
//s1.stepALE();
s1.movePoints();
s1.assemble();
s1.matMount();
s1.setUnCoupledBC();
s1.setGravity("-X");
s1.setBetaFlowLiq("+X");
s1.setRHS();
s1.setCopyDirectionPBC("RL");
s1.setInterfaceGeo();
//s1.setInterfaceLevelSet();
s1.unCoupledPBCNew();
//s1.unCoupledBetaPBC(); // rising-beta
if ( i%5 == 0 )
{
save.saveMSH(mshFolder,"newMesh",iter);
save.saveVTK(vtkFolder,"sim",iter);
save.saveVTKSurface(vtkFolder,"sim",iter);
save.saveSol(binFolder,"sim",iter);
save.saveBubbleInfo(datFolder);
//save.crossSectionalVoidFraction(datFolder,"voidFraction",iter);
save.saveBubbleShapeFactors(datFolder,"shapeFactors",iter);
}
s1.saveOldData();
cout << color(none,magenta,black);
cout << "________________________________________ END of "
<< iter << endl << endl;;
cout << resetColor();
s1.timeStep();
iter++;
}
Helmholtz3D h2(m1,h1);
h2.setBC();
//h2.initRisingBubble();
h2.initThreeBubbles();
h2.assemble();
h2.matMountC();
h2.setUnCoupledCBC();
h2.setCRHS();
h2.unCoupledC();
h2.setModel3DEdgeSize();
Model3D mOld = m1;
/* *********** MESH TREATMENT ************* */
// set normal and kappa values
m1.setNormalAndKappa();
m1.initMeshParameters();
// 3D operations
m1.insert3dMeshPointsByDiffusion(6.0);
m1.remove3dMeshPointsByDiffusion(0.5);
//m1.removePointByVolume();
//m1.removePointsByInterfaceDistance();
//m1.remove3dMeshPointsByDistance();
m1.remove3dMeshPointsByHeight();
m1.delete3DPoints();
// surface operations
m1.smoothPointsByCurvature();
m1.insertPointsByLength("curvature");
//m1.insertPointsByCurvature("flat");
//m1.removePointsByCurvature();
//m1.insertPointsByInterfaceDistance("flat");
m1.contractEdgesByLength("curvature");
//m1.removePointsByLength();
m1.flipTriangleEdges();
m1.removePointsByNeighbourCheck();
//m1.checkAngleBetweenPlanes();
/* **************************************** */
//m1.mesh2Dto3DOriginal();
m1.mesh3DPoints();
m1.setMapping();
#if NUMGLEU == 5
m1.setMiniElement();
#else
m1.setQuadElement();
#endif
m1.setSurfaceConfig();
if( strcmp( _frame,"moving") == 0 )
{
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC(vref);
pbc.MountPeriodicVectorsNew("print");
}
else
{
m1.setGenericBCPBCNew(physGroup);
m1.setGenericBC();
pbc.MountPeriodicVectorsNew("noPrint");
}
Simulator3D s2(m1,s1);
s2.applyLinearInterpolation(mOld);
s1 = s2;
s1.setSolverPressure(solverP);
s1.setSolverVelocity(solverV);
s1.setSolverConcentration(solverC);
InOut saveEnd(m1,s1); // cria objeto de gravacao
saveEnd.printMeshReport();
saveEnd.saveMeshInfo(datFolder);
}
PetscFinalize();
return 0;
}
/* compute forces */
static void force(mdsys_t *sys)
{
double epot;
epot = 0.0;
#if defined(_OPENMP)
#pragma omp parallel reduction(+:epot)
#endif
{
double c12,c6,boxby2,rcsq;
double *fx, *fy, *fz;
const double *rx, *ry, *rz;
int i, tid, fromidx, toidx, natoms;
/* precompute some constants */
c12 = 4.0*sys->epsilon*pow(sys->sigma,12.0);
c6 = 4.0*sys->epsilon*pow(sys->sigma, 6.0);
rcsq= sys->rcut * sys->rcut;
boxby2 = 0.5*sys->box;
natoms = sys->natoms;
epot = 0.0;
/* let each thread operate on a different
part of the enlarged force array */
#if defined(_OPENMP)
tid=omp_get_thread_num();
#else
tid=0;
#endif
fx=sys->frc + (3*tid*natoms);
azzero(fx,3*natoms);
fy=sys->frc + ((3*tid+1)*natoms);
fz=sys->frc + ((3*tid+2)*natoms);
rx=sys->pos;
ry=sys->pos + natoms;
rz=sys->pos + 2*natoms;
/* self interaction of atoms in cell */
for(i=0; i < sys->ncell; i += sys->nthreads) {
int j;
const cell_t *c1;
j = i + tid;
if (j >= (sys->ncell)) break;
c1=sys->clist + j;
for (j=0; j < c1->natoms-1; ++j) {
int ii,k;
double rx1, ry1, rz1;
ii=c1->idxlist[j];
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=j+1; k < c1->natoms; ++k) {
int jj;
double rx2,ry2,rz2,rsq;
jj=c1->idxlist[k];
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, sys->box);
ry2=pbc(ry1 - ry[jj], boxby2, sys->box);
rz2=pbc(rz1 - rz[jj], boxby2, sys->box);
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* interaction of atoms in different cells */
for(i=0; i < sys->npair; i += sys->nthreads) {
int j;
const cell_t *c1, *c2;
j = i + tid;
if (j >= (sys->npair)) break;
c1=sys->clist + sys->plist[2*j];
c2=sys->clist + sys->plist[2*j+1];
for (j=0; j < c1->natoms; ++j) {
int ii, k;
double rx1, ry1, rz1;
ii=c1->idxlist[j];
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=0; k < c2->natoms; ++k) {
int jj;
double rx2,ry2,rz2,rsq;
jj=c2->idxlist[k];
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, sys->box);
ry2=pbc(ry1 - ry[jj], boxby2, sys->box);
rz2=pbc(rz1 - rz[jj], boxby2, sys->box);
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* before reducing the forces, we have to make sure
that all threads are done adding to them. */
#if defined (_OPENMP)
#pragma omp barrier
#endif
/* set equal chunks of index ranges */
i = 1 + (3*natoms / sys->nthreads);
fromidx = tid * i;
toidx = fromidx + i;
if (toidx > 3*natoms) toidx = 3*natoms;
/* reduce forces from threads with tid != 0 into
the storage of the first thread. since we have
threads already spawned, we do this in parallel. */
for (i=1; i < sys->nthreads; ++i) {
int offs, j;
offs = 3*i*natoms;
for (j=fromidx; j < toidx; ++j) {
sys->frc[j] += sys->frc[offs+j];
}
}
}
sys->epot = epot;
}
