Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/KOKKOS/domain_kokkos.cpp
a641289d5ba3lammm-devel

Last Change
Raw File

domain_kokkos.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "domain_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "error.h"
#include "force.h"
#include "kspace.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
#define SMALL 1.0e-4
/* ---------------------------------------------------------------------- */
DomainKokkos::DomainKokkos(LAMMPS *lmp) : Domain(lmp) {}
/* ---------------------------------------------------------------------- */
void DomainKokkos::init()
{
atomKK = (AtomKokkos *) atom;
Domain::init();
}
/* ----------------------------------------------------------------------
reset global & local boxes due to global box boundary changes
if shrink-wrapped, determine atom extent and reset boxlo/hi
for triclinic, atoms must be in lamda coords (0-1) before reset_box is called
------------------------------------------------------------------------- */
template<class DeviceType>
struct DomainResetBoxFunctor{
public:
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array x;
struct value_type {
double value[3][2] ;
};
DomainResetBoxFunctor(DAT::tdual_x_array _x):
x(_x.view<DeviceType>()) {}
KOKKOS_INLINE_FUNCTION
void init(value_type &dst) const {
dst.value[2][0] = dst.value[1][0] = dst.value[0][0] = BIG;
dst.value[2][1] = dst.value[1][1] = dst.value[0][1] = -BIG;
}
KOKKOS_INLINE_FUNCTION
void join(volatile value_type &dst,
const volatile value_type &src) const {
dst.value[0][0] = MIN(dst.value[0][0],src.value[0][0]);
dst.value[0][1] = MAX(dst.value[0][1],src.value[0][1]);
dst.value[1][0] = MIN(dst.value[1][0],src.value[1][0]);
dst.value[1][1] = MAX(dst.value[1][1],src.value[1][1]);
dst.value[2][0] = MIN(dst.value[2][0],src.value[2][0]);
dst.value[2][1] = MAX(dst.value[2][1],src.value[2][1]);
}
KOKKOS_INLINE_FUNCTION
void operator() (const int &i, value_type &dst) const {
dst.value[0][0] = MIN(dst.value[0][0],x(i,0));
dst.value[0][1] = MAX(dst.value[0][1],x(i,0));
dst.value[1][0] = MIN(dst.value[1][0],x(i,1));
dst.value[1][1] = MAX(dst.value[1][1],x(i,1));
dst.value[2][0] = MIN(dst.value[2][0],x(i,2));
dst.value[2][1] = MAX(dst.value[2][1],x(i,2));
}
};
void DomainKokkos::reset_box()
{
// perform shrink-wrapping
// compute extent of atoms on this proc
// for triclinic, this is done in lamda space
atomKK->sync(Device,X_MASK);
if (nonperiodic == 2) {
int nlocal = atom->nlocal;
DomainResetBoxFunctor<LMPDeviceType>::value_type result;
DomainResetBoxFunctor<LMPDeviceType>
f(atomKK->k_x);
Kokkos::parallel_reduce(nlocal,f,result);
LMPDeviceType::fence();
double (*extent)[2] = result.value;
double all[3][2];
// compute extent across all procs
// flip sign of MIN to do it in one Allreduce MAX
extent[0][0] = -extent[0][0];
extent[1][0] = -extent[1][0];
extent[2][0] = -extent[2][0];
MPI_Allreduce(extent,all,6,MPI_DOUBLE,MPI_MAX,world);
// for triclinic, convert back to box coords before changing box
if (triclinic) lamda2x(atom->nlocal);
// in shrink-wrapped dims, set box by atom extent
// if minimum set, enforce min box size settings
// for triclinic, convert lamda extent to box coords, then set box lo/hi
// decided NOT to do the next comment - don't want to sneakily change tilt
// for triclinic, adjust tilt factors if 2nd dim is shrink-wrapped,
// so that displacement in 1st dim stays the same
if (triclinic == 0) {
if (xperiodic == 0) {
if (boundary[0][0] == 2) boxlo[0] = -all[0][0] - small[0];
else if (boundary[0][0] == 3)
boxlo[0] = MIN(-all[0][0]-small[0],minxlo);
if (boundary[0][1] == 2) boxhi[0] = all[0][1] + small[0];
else if (boundary[0][1] == 3) boxhi[0] = MAX(all[0][1]+small[0],minxhi);
if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
}
if (yperiodic == 0) {
if (boundary[1][0] == 2) boxlo[1] = -all[1][0] - small[1];
else if (boundary[1][0] == 3)
boxlo[1] = MIN(-all[1][0]-small[1],minylo);
if (boundary[1][1] == 2) boxhi[1] = all[1][1] + small[1];
else if (boundary[1][1] == 3) boxhi[1] = MAX(all[1][1]+small[1],minyhi);
if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
}
if (zperiodic == 0) {
if (boundary[2][0] == 2) boxlo[2] = -all[2][0] - small[2];
else if (boundary[2][0] == 3)
boxlo[2] = MIN(-all[2][0]-small[2],minzlo);
if (boundary[2][1] == 2) boxhi[2] = all[2][1] + small[2];
else if (boundary[2][1] == 3) boxhi[2] = MAX(all[2][1]+small[2],minzhi);
if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
}
} else {
double lo[3],hi[3];
if (xperiodic == 0) {
lo[0] = -all[0][0]; lo[1] = 0.0; lo[2] = 0.0;
Domain::lamda2x(lo,lo);
hi[0] = all[0][1]; hi[1] = 0.0; hi[2] = 0.0;
Domain::lamda2x(hi,hi);
if (boundary[0][0] == 2) boxlo[0] = lo[0] - small[0];
else if (boundary[0][0] == 3) boxlo[0] = MIN(lo[0]-small[0],minxlo);
if (boundary[0][1] == 2) boxhi[0] = hi[0] + small[0];
else if (boundary[0][1] == 3) boxhi[0] = MAX(hi[0]+small[0],minxhi);
if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
}
if (yperiodic == 0) {
lo[0] = 0.0; lo[1] = -all[1][0]; lo[2] = 0.0;
Domain::lamda2x(lo,lo);
hi[0] = 0.0; hi[1] = all[1][1]; hi[2] = 0.0;
Domain::lamda2x(hi,hi);
if (boundary[1][0] == 2) boxlo[1] = lo[1] - small[1];
else if (boundary[1][0] == 3) boxlo[1] = MIN(lo[1]-small[1],minylo);
if (boundary[1][1] == 2) boxhi[1] = hi[1] + small[1];
else if (boundary[1][1] == 3) boxhi[1] = MAX(hi[1]+small[1],minyhi);
if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
//xy *= (boxhi[1]-boxlo[1]) / yprd;
}
if (zperiodic == 0) {
lo[0] = 0.0; lo[1] = 0.0; lo[2] = -all[2][0];
Domain::lamda2x(lo,lo);
hi[0] = 0.0; hi[1] = 0.0; hi[2] = all[2][1];
Domain::lamda2x(hi,hi);
if (boundary[2][0] == 2) boxlo[2] = lo[2] - small[2];
else if (boundary[2][0] == 3) boxlo[2] = MIN(lo[2]-small[2],minzlo);
if (boundary[2][1] == 2) boxhi[2] = hi[2] + small[2];
else if (boundary[2][1] == 3) boxhi[2] = MAX(hi[2]+small[2],minzhi);
if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
//xz *= (boxhi[2]-boxlo[2]) / xprd;
//yz *= (boxhi[2]-boxlo[2]) / yprd;
}
}
}
// reset box whether shrink-wrapping or not
set_global_box();
set_local_box();
// if shrink-wrapped & kspace is defined (i.e. using MSM), call setup()
// also call init() (to test for compatibility) ?
if (nonperiodic == 2 && force->kspace) {
//force->kspace->init();
force->kspace->setup();
}
// if shrink-wrapped & triclinic, re-convert to lamda coords for new box
// re-invoke pbc() b/c x2lamda result can be outside [0,1] due to roundoff
if (nonperiodic == 2 && triclinic) {
x2lamda(atom->nlocal);
pbc();
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType, int PERIODIC, int DEFORM_VREMAP>
struct DomainPBCFunctor {
typedef DeviceType device_type;
double lo[3],hi[3],period[3];
typename ArrayTypes<DeviceType>::t_x_array x;
typename ArrayTypes<DeviceType>::t_v_array v;
typename ArrayTypes<DeviceType>::t_int_1d mask;
typename ArrayTypes<DeviceType>::t_imageint_1d image;
int deform_groupbit;
double h_rate[6];
int xperiodic,yperiodic,zperiodic;
DomainPBCFunctor(double* _lo, double* _hi, double* _period,
DAT::tdual_x_array _x, DAT::tdual_v_array _v,
DAT::tdual_int_1d _mask, DAT::tdual_imageint_1d _image,
int _deform_groupbit, double* _h_rate,
int _xperiodic, int _yperiodic, int _zperiodic):
x(_x.view<DeviceType>()), v(_v.view<DeviceType>()),
mask(_mask.view<DeviceType>()), image(_image.view<DeviceType>()),
deform_groupbit(_deform_groupbit),
xperiodic(_xperiodic), yperiodic(_yperiodic), zperiodic(_zperiodic){
lo[0]=_lo[0]; lo[1]=_lo[1]; lo[2]=_lo[2];
hi[0]=_hi[0]; hi[1]=_hi[1]; hi[2]=_hi[2];
period[0]=_period[0]; period[1]=_period[1]; period[2]=_period[2];
h_rate[0]=_h_rate[0]; h_rate[1]=_h_rate[1]; h_rate[2]=_h_rate[2];
h_rate[3]=_h_rate[3]; h_rate[4]=_h_rate[4]; h_rate[5]=_h_rate[5];
}
KOKKOS_INLINE_FUNCTION
void operator() (const int &i) const {
if (PERIODIC && xperiodic) {
if (x(i,0) < lo[0]) {
x(i,0) += period[0];
if (DEFORM_VREMAP && (mask[i] & deform_groupbit)) v(i,0) += h_rate[0];
imageint idim = image[i] & IMGMASK;
const imageint otherdims = image[i] ^ idim;
idim--;
idim &= IMGMASK;
image[i] = otherdims | idim;
}
if (x(i,0) >= hi[0]) {
x(i,0) -= period[0];
x(i,0) = MAX(x(i,0),lo[0]);
if (DEFORM_VREMAP && (mask[i] & deform_groupbit)) v(i,0) -= h_rate[0];
imageint idim = image[i] & IMGMASK;
const imageint otherdims = image[i] ^ idim;
idim++;
idim &= IMGMASK;
image[i] = otherdims | idim;
}
}
if (PERIODIC && yperiodic) {
if (x(i,1) < lo[1]) {
x(i,1) += period[1];
if (DEFORM_VREMAP && (mask[i] & deform_groupbit)) {
v(i,0) += h_rate[5];
v(i,1) += h_rate[1];
}
imageint idim = (image[i] >> IMGBITS) & IMGMASK;
const imageint otherdims = image[i] ^ (idim << IMGBITS);
idim--;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMGBITS);
}
if (x(i,1) >= hi[1]) {
x(i,1) -= period[1];
x(i,1) = MAX(x(i,1),lo[1]);
if (DEFORM_VREMAP && (mask[i] & deform_groupbit)) {
v(i,0) -= h_rate[5];
v(i,1) -= h_rate[1];
}
imageint idim = (image[i] >> IMGBITS) & IMGMASK;
const imageint otherdims = image[i] ^ (idim << IMGBITS);
idim++;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMGBITS);
}
}
if (PERIODIC && zperiodic) {
if (x(i,2) < lo[2]) {
x(i,2) += period[2];
if (DEFORM_VREMAP && (mask[i] & deform_groupbit)) {
v(i,0) += h_rate[4];
v(i,1) += h_rate[3];
v(i,2) += h_rate[2];
}
imageint idim = image[i] >> IMG2BITS;
const imageint otherdims = image[i] ^ (idim << IMG2BITS);
idim--;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMG2BITS);
}
if (x(i,2) >= hi[2]) {
x(i,2) -= period[2];
x(i,2) = MAX(x(i,2),lo[2]);
if (DEFORM_VREMAP && (mask[i] & deform_groupbit)) {
v(i,0) -= h_rate[4];
v(i,1) -= h_rate[3];
v(i,2) -= h_rate[2];
}
imageint idim = image[i] >> IMG2BITS;
const imageint otherdims = image[i] ^ (idim << IMG2BITS);
idim++;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMG2BITS);
}
}
}
};
/* ----------------------------------------------------------------------
enforce PBC and modify box image flags for each atom
called every reneighboring and by other commands that change atoms
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
if fix deform, remap velocity of fix group atoms by box edge velocities
for triclinic, atoms must be in lamda coords (0-1) before pbc is called
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */
void DomainKokkos::pbc()
{
double *lo,*hi,*period;
int nlocal = atomKK->nlocal;
if (triclinic == 0) {
lo = boxlo;
hi = boxhi;
period = prd;
} else {
lo = boxlo_lamda;
hi = boxhi_lamda;
period = prd_lamda;
}
atomKK->sync(Device,X_MASK|V_MASK|MASK_MASK|IMAGE_MASK);
if (xperiodic || yperiodic || zperiodic) {
if (deform_vremap) {
DomainPBCFunctor<LMPDeviceType,1,1>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
Kokkos::parallel_for(nlocal,f);
} else {
DomainPBCFunctor<LMPDeviceType,1,0>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
Kokkos::parallel_for(nlocal,f);
}
} else {
if (deform_vremap) {
DomainPBCFunctor<LMPDeviceType,0,1>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
Kokkos::parallel_for(nlocal,f);
} else {
DomainPBCFunctor<LMPDeviceType,0,0>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
Kokkos::parallel_for(nlocal,f);
}
}
LMPDeviceType::fence();
atomKK->modified(Device,X_MASK|V_MASK|IMAGE_MASK);
}
/* ----------------------------------------------------------------------
remap all points into the periodic box no matter how far away
adjust 3 image flags encoded in image accordingly
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
for triclinic, point is converted to lamda coords (0-1) before doing remap
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */
void DomainKokkos::remap_all()
{
atomKK->sync(Device,X_MASK | IMAGE_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
image = atomKK->k_image.view<LMPDeviceType>();
int nlocal = atomKK->nlocal;
if (triclinic == 0) {
for (int i=0; i<3; i++) {
lo[i] = boxlo[i];
hi[i] = boxhi[i];
period[i] = prd[i];
}
} else {
for (int i=0; i<3; i++) {
lo[i] = boxlo_lamda[i];
hi[i] = boxhi_lamda[i];
period[i] = prd_lamda[i];
}
x2lamda(nlocal);
}
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_remap_all>(0,nlocal),*this);
LMPDeviceType::fence();
copymode = 0;
atomKK->modified(Device,X_MASK | IMAGE_MASK);
if (triclinic) lamda2x(nlocal);
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_remap_all, const int &i) const {
imageint idim,otherdims;
if (xperiodic) {
while (x(i,0) < lo[0]) {
x(i,0) += period[0];
idim = image[i] & IMGMASK;
otherdims = image[i] ^ idim;
idim--;
idim &= IMGMASK;
image[i] = otherdims | idim;
}
while (x(i,0) >= hi[0]) {
x(i,0) -= period[0];
idim = image[i] & IMGMASK;
otherdims = image[i] ^ idim;
idim++;
idim &= IMGMASK;
image[i] = otherdims | idim;
}
x(i,0) = MAX(x(i,0),lo[0]);
}
if (yperiodic) {
while (x(i,1) < lo[1]) {
x(i,1) += period[1];
idim = (image[i] >> IMGBITS) & IMGMASK;
otherdims = image[i] ^ (idim << IMGBITS);
idim--;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMGBITS);
}
while (x(i,1) >= hi[1]) {
x(i,1) -= period[1];
idim = (image[i] >> IMGBITS) & IMGMASK;
otherdims = image[i] ^ (idim << IMGBITS);
idim++;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMGBITS);
}
x(i,1) = MAX(x(i,1),lo[1]);
}
if (zperiodic) {
while (x(i,2) < lo[2]) {
x(i,2) += period[2];
idim = image[i] >> IMG2BITS;
otherdims = image[i] ^ (idim << IMG2BITS);
idim--;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMG2BITS);
}
while (x(i,2) >= hi[2]) {
x(i,2) -= period[2];
idim = image[i] >> IMG2BITS;
otherdims = image[i] ^ (idim << IMG2BITS);
idim++;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMG2BITS);
}
x(i,2) = MAX(x(i,2),lo[2]);
}
}
/* ----------------------------------------------------------------------
adjust image flags due to triclinic box flip
flip operation is changing box vectors A,B,C to new A',B',C'
A' = A (A does not change)
B' = B + mA (B shifted by A)
C' = C + pB + nA (C shifted by B and/or A)
this requires the image flags change from (a,b,c) to (a',b',c')
so that x_unwrap for each atom is same before/after
x_unwrap_before = xlocal + aA + bB + cC
x_unwrap_after = xlocal + a'A' + b'B' + c'C'
this requires:
c' = c
b' = b - cp
a' = a - (b-cp)m - cn = a - b'm - cn
in other words, for xy flip, change in x flag depends on current y flag
this is b/c the xy flip dramatically changes which tiled image of
simulation box an unwrapped point maps to
------------------------------------------------------------------------- */
void DomainKokkos::image_flip(int m_in, int n_in, int p_in)
{
m_flip = m_in;
n_flip = n_in;
p_flip = p_in;
atomKK->sync(Device,IMAGE_MASK);
image = atomKK->k_image.view<LMPDeviceType>();
int nlocal = atomKK->nlocal;
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_image_flip>(0,nlocal),*this);
LMPDeviceType::fence();
copymode = 0;
atomKK->modified(Device,IMAGE_MASK);
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_image_flip, const int &i) const {
int xbox = (image[i] & IMGMASK) - IMGMAX;
int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int zbox = (image[i] >> IMG2BITS) - IMGMAX;
ybox -= p_flip*zbox;
xbox -= m_flip*ybox + n_flip*zbox;
image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
/* ----------------------------------------------------------------------
convert triclinic 0-1 lamda coords to box coords for all N atoms
x = H lamda + x0;
------------------------------------------------------------------------- */
void DomainKokkos::lamda2x(int n)
{
atomKK->sync(Device,X_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_lamda2x>(0,n),*this);
LMPDeviceType::fence();
copymode = 0;
atomKK->modified(Device,X_MASK);
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_lamda2x, const int &i) const {
x(i,0) = h[0]*x(i,0) + h[5]*x(i,1) + h[4]*x(i,2) + boxlo[0];
x(i,1) = h[1]*x(i,1) + h[3]*x(i,2) + boxlo[1];
x(i,2) = h[2]*x(i,2) + boxlo[2];
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for all N atoms
lamda = H^-1 (x - x0)
------------------------------------------------------------------------- */
void DomainKokkos::x2lamda(int n)
{
atomKK->sync(Device,X_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_x2lamda>(0,n),*this);
LMPDeviceType::fence();
copymode = 0;
atomKK->modified(Device,X_MASK);
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_x2lamda, const int &i) const {
F_FLOAT delta[3];
delta[0] = x(i,0) - boxlo[0];
delta[1] = x(i,1) - boxlo[1];
delta[2] = x(i,2) - boxlo[2];
x(i,0) = h_inv[0]*delta[0] + h_inv[5]*delta[1] + h_inv[4]*delta[2];
x(i,1) = h_inv[1]*delta[1] + h_inv[3]*delta[2];
x(i,2) = h_inv[2]*delta[2];
}
c4science · Help