Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/KOKKOS/dihedral_class2_kokkos.cpp
7edb294b447clammm-devel

Last Change
Raw File

dihedral_class2_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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "dihedral_class2_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
#include "neighbor_kokkos.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
template<class DeviceType>
DihedralClass2Kokkos<DeviceType>::DihedralClass2Kokkos(LAMMPS *lmp) : DihedralClass2(lmp)
{
atomKK = (AtomKokkos *) atom;
neighborKK = (NeighborKokkos *) neighbor;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
k_warning_flag = DAT::tdual_int_scalar("Dihedral:warning_flag");
d_warning_flag = k_warning_flag.view<DeviceType>();
h_warning_flag = k_warning_flag.h_view;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
DihedralClass2Kokkos<DeviceType>::~DihedralClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void DihedralClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (eflag || vflag) ev_setup(eflag,vflag,0);
else evflag = 0;
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
//atomKK->sync(execution_space,datamask_read);
k_k1.template sync<DeviceType>();
k_k2.template sync<DeviceType>();
k_k3.template sync<DeviceType>();
k_phi1.template sync<DeviceType>();
k_phi2.template sync<DeviceType>();
k_phi3.template sync<DeviceType>();
k_mbt_f1.template sync<DeviceType>();
k_mbt_f2.template sync<DeviceType>();
k_mbt_f3.template sync<DeviceType>();
k_mbt_r0.template sync<DeviceType>();
k_ebt_f1_1.template sync<DeviceType>();
k_ebt_f2_1.template sync<DeviceType>();
k_ebt_f3_1.template sync<DeviceType>();
k_ebt_r0_1.template sync<DeviceType>();
k_ebt_f1_2.template sync<DeviceType>();
k_ebt_f2_2.template sync<DeviceType>();
k_ebt_f3_2.template sync<DeviceType>();
k_ebt_r0_2.template sync<DeviceType>();
k_at_f1_1.template sync<DeviceType>();
k_at_f2_1.template sync<DeviceType>();
k_at_f3_1.template sync<DeviceType>();
k_at_f1_2.template sync<DeviceType>();
k_at_f2_2.template sync<DeviceType>();
k_at_f3_2.template sync<DeviceType>();
k_at_theta0_1.template sync<DeviceType>();
k_at_theta0_2.template sync<DeviceType>();
k_aat_k.template sync<DeviceType>();
k_aat_theta0_1.template sync<DeviceType>();
k_aat_theta0_2.template sync<DeviceType>();
k_bb13t_k.template sync<DeviceType>();
k_bb13t_r10.template sync<DeviceType>();
k_bb13t_r30.template sync<DeviceType>();
k_setflag_d.template sync<DeviceType>();
k_setflag_mbt.template sync<DeviceType>();
k_setflag_ebt.template sync<DeviceType>();
k_setflag_at.template sync<DeviceType>();
k_setflag_aat.template sync<DeviceType>();
k_setflag_bb13t.template sync<DeviceType>();
//if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
//else atomKK->modified(execution_space,F_MASK);
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
neighborKK->k_dihedrallist.template sync<DeviceType>();
dihedrallist = neighborKK->k_dihedrallist.view<DeviceType>();
int ndihedrallist = neighborKK->ndihedrallist;
nlocal = atom->nlocal;
newton_bond = force->newton_bond;
h_warning_flag() = 0;
k_warning_flag.template modify<LMPHostType>();
k_warning_flag.template sync<DeviceType>();
copymode = 1;
// loop over neighbors of my atoms
EV_FLOAT ev;
if (evflag) {
if (newton_bond) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<1,1> >(0,ndihedrallist),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<0,1> >(0,ndihedrallist),*this,ev);
}
} else {
if (newton_bond) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<1,0> >(0,ndihedrallist),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagDihedralClass2Compute<0,0> >(0,ndihedrallist),*this);
}
}
// error check
k_warning_flag.template modify<DeviceType>();
k_warning_flag.template sync<LMPHostType>();
if (h_warning_flag())
error->warning(FLERR,"Dihedral problem",0);
if (eflag_global) energy += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
virial[1] += ev.v[1];
virial[2] += ev.v[2];
virial[3] += ev.v[3];
virial[4] += ev.v[4];
virial[5] += ev.v[5];
}
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
copymode = 0;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
// The f array is atomic
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > a_f = f;
const int i1 = dihedrallist(n,0);
const int i2 = dihedrallist(n,1);
const int i3 = dihedrallist(n,2);
const int i4 = dihedrallist(n,3);
const int type = dihedrallist(n,4);
// 1st bond
const F_FLOAT vb1x = x(i1,0) - x(i2,0);
const F_FLOAT vb1y = x(i1,1) - x(i2,1);
const F_FLOAT vb1z = x(i1,2) - x(i2,2);
// 2nd bond
const F_FLOAT vb2x = x(i3,0) - x(i2,0);
const F_FLOAT vb2y = x(i3,1) - x(i2,1);
const F_FLOAT vb2z = x(i3,2) - x(i2,2);
const F_FLOAT vb2xm = -vb2x;
const F_FLOAT vb2ym = -vb2y;
const F_FLOAT vb2zm = -vb2z;
// 3rd bond
const F_FLOAT vb3x = x(i4,0) - x(i3,0);
const F_FLOAT vb3y = x(i4,1) - x(i3,1);
const F_FLOAT vb3z = x(i4,2) - x(i3,2);
// distance: c0 calculation
const F_FLOAT r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
const F_FLOAT r1 = sqrt(r1mag2);
const F_FLOAT r2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
const F_FLOAT r2 = sqrt(r2mag2);
const F_FLOAT r3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
const F_FLOAT r3 = sqrt(r3mag2);
const F_FLOAT sb1 = 1.0/r1mag2;
const F_FLOAT rb1 = 1.0/r1;
const F_FLOAT sb2 = 1.0/r2mag2;
const F_FLOAT rb2 = 1.0/r2;
const F_FLOAT sb3 = 1.0/r3mag2;
const F_FLOAT rb3 = 1.0/r3;
const F_FLOAT c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
const F_FLOAT r12c1 = rb1*rb2;
const F_FLOAT r12c2 = rb2*rb3;
const F_FLOAT costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
const F_FLOAT costh13 = c0;
const F_FLOAT costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
// cos and sin of 2 angles and final c
F_FLOAT sin2 = MAX(1.0 - costh12*costh12,0.0);
F_FLOAT sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - costh23*costh23,0.0);
F_FLOAT sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
const F_FLOAT s1 = sc1 * sc1;
const F_FLOAT s2 = sc2 * sc2;
const F_FLOAT s12 = sc1 * sc2;
F_FLOAT c = (c0 + costh12*costh23) * s12;
// error check
if ((c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) && !d_warning_flag())
Kokkos::atomic_fetch_add(&d_warning_flag(),1);
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
const F_FLOAT cosphi = c;
F_FLOAT phi = acos(c);
F_FLOAT sinphi = sqrt(1.0 - c*c);
sinphi = MAX(sinphi,SMALL);
// n123 = vb1 x vb2
const F_FLOAT n123x = vb1y*vb2z - vb1z*vb2y;
const F_FLOAT n123y = vb1z*vb2x - vb1x*vb2z;
const F_FLOAT n123z = vb1x*vb2y - vb1y*vb2x;
const F_FLOAT n123_dot_vb3 = n123x*vb3x + n123y*vb3y + n123z*vb3z;
if (n123_dot_vb3 > 0.0) {
phi = -phi;
sinphi = -sinphi;
}
const F_FLOAT a11 = -c*sb1*s1;
const F_FLOAT a22 = sb2 * (2.0*costh13*s12 - c*(s1+s2));
const F_FLOAT a33 = -c*sb3*s2;
const F_FLOAT a12 = r12c1 * (costh12*c*s1 + costh23*s12);
const F_FLOAT a13 = rb1*rb3*s12;
const F_FLOAT a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
const F_FLOAT sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
const F_FLOAT sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
const F_FLOAT sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
const F_FLOAT sy1 = a11*vb1y + a12*vb2y + a13*vb3y;
const F_FLOAT sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
const F_FLOAT sy12 = a13*vb1y + a23*vb2y + a33*vb3y;
const F_FLOAT sz1 = a11*vb1z + a12*vb2z + a13*vb3z;
const F_FLOAT sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
const F_FLOAT sz12 = a13*vb1z + a23*vb2z + a33*vb3z;
// set up d(cos(phi))/d(r) and dphi/dr arrays
F_FLOAT dcosphidr[4][3], dphidr[4][3];
dcosphidr[0][0] = -sx1;
dcosphidr[0][1] = -sy1;
dcosphidr[0][2] = -sz1;
dcosphidr[1][0] = sx2 + sx1;
dcosphidr[1][1] = sy2 + sy1;
dcosphidr[1][2] = sz2 + sz1;
dcosphidr[2][0] = sx12 - sx2;
dcosphidr[2][1] = sy12 - sy2;
dcosphidr[2][2] = sz12 - sz2;
dcosphidr[3][0] = -sx12;
dcosphidr[3][1] = -sy12;
dcosphidr[3][2] = -sz12;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
F_FLOAT edihedral = 0.0;
const F_FLOAT dphi1 = phi - d_phi1[type];
const F_FLOAT dphi2 = 2.0*phi - d_phi2[type];
const F_FLOAT dphi3 = 3.0*phi - d_phi3[type];
if (eflag) edihedral = d_k1[type]*(1.0 - cos(dphi1)) +
d_k2[type]*(1.0 - cos(dphi2)) +
d_k3[type]*(1.0 - cos(dphi3));
const F_FLOAT de_dihedral = d_k1[type]*sin(dphi1) + 2.0*d_k2[type]*sin(dphi2) +
3.0*d_k3[type]*sin(dphi3);
// torsion forces on all 4 atoms
F_FLOAT dbonddr[3][4][3], fabcd[4][3];
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (int i = 0; i < 3; i++)
for (int j = 0; j < 4; j++)
for (int k = 0; k < 3; k++)
dbonddr[i][j][k] = 0.0;
// bond1
dbonddr[0][0][0] = vb1x / r1;
dbonddr[0][0][1] = vb1y / r1;
dbonddr[0][0][2] = vb1z / r1;
dbonddr[0][1][0] = -vb1x / r1;
dbonddr[0][1][1] = -vb1y / r1;
dbonddr[0][1][2] = -vb1z / r1;
// bond2
dbonddr[1][1][0] = vb2x / r2;
dbonddr[1][1][1] = vb2y / r2;
dbonddr[1][1][2] = vb2z / r2;
dbonddr[1][2][0] = -vb2x / r2;
dbonddr[1][2][1] = -vb2y / r2;
dbonddr[1][2][2] = -vb2z / r2;
// bond3
dbonddr[2][2][0] = vb3x / r3;
dbonddr[2][2][1] = vb3y / r3;
dbonddr[2][2][2] = vb3z / r3;
dbonddr[2][3][0] = -vb3x / r3;
dbonddr[2][3][1] = -vb3y / r3;
dbonddr[2][3][2] = -vb3z / r3;
// set up d(theta)/d(r) array
// dthetadr(i,j,k) = angle i, atom j, coordinate k
F_FLOAT dthetadr[2][4][3];
for (int i = 0; i < 2; i++)
for (int j = 0; j < 4; j++)
for (int k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
const F_FLOAT t1 = costh12 / r1mag2;
const F_FLOAT t2 = costh23 / r2mag2;
const F_FLOAT t3 = costh12 / r2mag2;
const F_FLOAT t4 = costh23 / r3mag2;
// angle12
dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
(-t3 * vb2x) + (vb1x * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
(-t3 * vb2y) + (vb1y * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
(-t3 * vb2z) + (vb1z * r12c1));
dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
// angle23
dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
(t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
(t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
(t4 * vb3z) + (vb2z * r12c2));
dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
F_FLOAT cos2phi = cos(2.0*phi);
F_FLOAT cos3phi = cos(3.0*phi);
F_FLOAT bt1 = d_mbt_f1[type] * cosphi;
F_FLOAT bt2 = d_mbt_f2[type] * cos2phi;
F_FLOAT bt3 = d_mbt_f3[type] * cos3phi;
F_FLOAT sumbte = bt1 + bt2 + bt3;
F_FLOAT db = r2 - d_mbt_r0[type];
if (eflag) edihedral += db * sumbte;
// force on bond2
bt1 = -d_mbt_f1[type] * sinphi;
bt2 = -2.0 * d_mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * d_mbt_f3[type] * sin(3.0*phi);
F_FLOAT sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
bt1 = d_ebt_f1_1[type] * cosphi;
bt2 = d_ebt_f2_1[type] * cos2phi;
bt3 = d_ebt_f3_1[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r1 - d_ebt_r0_1[type];
if (eflag) edihedral += db * (bt1+bt2+bt3);
// force on bond1
bt1 = d_ebt_f1_1[type] * sinphi;
bt2 = 2.0 * d_ebt_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * d_ebt_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
bt1 = d_ebt_f1_2[type] * cosphi;
bt2 = d_ebt_f2_2[type] * cos2phi;
bt3 = d_ebt_f3_2[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r3 - d_ebt_r0_2[type];
if (eflag) edihedral += db * (bt1+bt2+bt3);
// force on bond3
bt1 = -d_ebt_f1_2[type] * sinphi;
bt2 = -2.0 * d_ebt_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * d_ebt_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
F_FLOAT at1 = d_at_f1_1[type] * cosphi;
F_FLOAT at2 = d_at_f2_1[type] * cos2phi;
F_FLOAT at3 = d_at_f3_1[type] * cos3phi;
sumbte = at1 + at2 + at3;
F_FLOAT da = acos(costh12) - d_at_theta0_1[type];
if (eflag) edihedral += da * (at1+at2+at3);
// force on angle1
bt1 = d_at_f1_1[type] * sinphi;
bt2 = 2.0 * d_at_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * d_at_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
at1 = d_at_f1_2[type] * cosphi;
at2 = d_at_f2_2[type] * cos2phi;
at3 = d_at_f3_2[type] * cos3phi;
sumbte = at1 + at2 + at3;
da = acos(costh23) - d_at_theta0_2[type];
if (eflag) edihedral += da * (at1+at2+at3);
// force on angle2
bt1 = -d_at_f1_2[type] * sinphi;
bt2 = -2.0 * d_at_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * d_at_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
const F_FLOAT da1 = acos(costh12) - d_aat_theta0_1[type];
const F_FLOAT da2 = acos(costh23) - d_aat_theta0_2[type];
if (eflag) edihedral += d_aat_k[type]*da1*da2*cosphi;
for (int i = 0; i < 4; i++)
for (int j = 0; j < 3; j++)
fabcd[i][j] -= d_aat_k[type] *
(cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
if (fabs(d_bb13t_k[type]) > SMALL) {
const F_FLOAT r1_0 = d_bb13t_r10[type];
const F_FLOAT r3_0 = d_bb13t_r30[type];
const F_FLOAT dr1 = r1 - r1_0;
const F_FLOAT dr2 = r3 - r3_0;
const F_FLOAT tk1 = -d_bb13t_k[type] * dr1 / r3;
const F_FLOAT tk2 = -d_bb13t_k[type] * dr2 / r1;
if (eflag) edihedral += d_bb13t_k[type]*dr1*dr2;
fabcd[0][0] += tk2 * vb1x;
fabcd[0][1] += tk2 * vb1y;
fabcd[0][2] += tk2 * vb1z;
fabcd[1][0] -= tk2 * vb1x;
fabcd[1][1] -= tk2 * vb1y;
fabcd[1][2] -= tk2 * vb1z;
fabcd[2][0] -= tk1 * vb3x;
fabcd[2][1] -= tk1 * vb3y;
fabcd[2][2] -= tk1 * vb3z;
fabcd[3][0] += tk1 * vb3x;
fabcd[3][1] += tk1 * vb3y;
fabcd[3][2] += tk1 * vb3z;
}
F_FLOAT f1[3],f2[3],f3[3],f4[3];
for (int i = 0; i < 3; i++) {
f1[i] = fabcd[0][i];
f2[i] = fabcd[1][i];
f3[i] = fabcd[2][i];
f4[i] = fabcd[3][i];
}
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
a_f(i1,0) += f1[0];
a_f(i1,1) += f1[1];
a_f(i1,2) += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
a_f(i2,0) += f2[0];
a_f(i2,1) += f2[1];
a_f(i2,2) += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
a_f(i3,0) += f3[0];
a_f(i3,1) += f3[1];
a_f(i3,2) += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
a_f(i4,0) += f4[0];
a_f(i4,1) += f4[1];
a_f(i4,2) += f4[2];
}
if (EVFLAG)
ev_tally(ev,i1,i2,i3,i4,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEWTON_BOND, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void DihedralClass2Kokkos<DeviceType>::operator()(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>, const int &n) const {
EV_FLOAT ev;
this->template operator()<NEWTON_BOND,EVFLAG>(TagDihedralClass2Compute<NEWTON_BOND,EVFLAG>(), n, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void DihedralClass2Kokkos<DeviceType>::allocate()
{
DihedralClass2::allocate();
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
template<class DeviceType>
void DihedralClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
{
DihedralClass2::coeff(narg, arg);
int n = atom->ndihedraltypes;
k_k1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::k1",n+1);
k_k2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::k2",n+1);
k_k3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::k3",n+1);
k_phi1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::phi1",n+1);
k_phi2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::phi2",n+1);
k_phi3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::phi3",n+1);
k_mbt_f1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_f1",n+1);
k_mbt_f2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_f2",n+1);
k_mbt_f3 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_f3",n+1);
k_mbt_r0 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::mbt_r0",n+1);
k_ebt_f1_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f1_1",n+1);
k_ebt_f2_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f2_1",n+1);
k_ebt_f3_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f3_1",n+1);
k_ebt_r0_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_r0_1",n+1);
k_ebt_f1_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f1_2",n+1);
k_ebt_f2_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f2_2",n+1);
k_ebt_f3_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_f3_2",n+1);
k_ebt_r0_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::ebt_r0_2",n+1);
k_at_f1_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f1_1",n+1);
k_at_f2_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f2_1",n+1);
k_at_f3_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f3_1",n+1);
k_at_f1_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f1_2",n+1);
k_at_f2_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f2_2",n+1);
k_at_f3_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_f3_2",n+1);
k_at_theta0_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_theta0_1",n+1);
k_at_theta0_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::at_theta0_2",n+1);
k_aat_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::aat_k",n+1);
k_aat_theta0_1 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::aat_theta0_1",n+1);
k_aat_theta0_2 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::aat_theta0_2",n+1);
k_bb13t_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::bb13t_k",n+1);
k_bb13t_r10 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::bb13t_r10",n+1);
k_bb13t_r30 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("DihedralClass2::bb13t_r30",n+1);
k_setflag_d = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_d",n+1);
k_setflag_mbt = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_mbt",n+1);
k_setflag_ebt = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_ebt",n+1);
k_setflag_at = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_at",n+1);
k_setflag_aat = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_aat",n+1);
k_setflag_bb13t = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleClass2::setflag_bb13t",n+1);
d_k1 = k_k1.template view<DeviceType>();
d_k2 = k_k2.template view<DeviceType>();
d_k3 = k_k3.template view<DeviceType>();
d_phi1 = k_phi1.template view<DeviceType>();
d_phi2 = k_phi2.template view<DeviceType>();
d_phi3 = k_phi3.template view<DeviceType>();
d_mbt_f1 = k_mbt_f1.template view<DeviceType>();
d_mbt_f2 = k_mbt_f2.template view<DeviceType>();
d_mbt_f3 = k_mbt_f3.template view<DeviceType>();
d_mbt_r0 = k_mbt_r0.template view<DeviceType>();
d_ebt_f1_1 = k_ebt_f1_1.template view<DeviceType>();
d_ebt_f2_1 = k_ebt_f2_1.template view<DeviceType>();
d_ebt_f3_1 = k_ebt_f3_1.template view<DeviceType>();
d_ebt_r0_1 = k_ebt_r0_1.template view<DeviceType>();
d_ebt_f1_2 = k_ebt_f1_2.template view<DeviceType>();
d_ebt_f2_2 = k_ebt_f2_2.template view<DeviceType>();
d_ebt_f3_2 = k_ebt_f3_2.template view<DeviceType>();
d_ebt_r0_2 = k_ebt_r0_2.template view<DeviceType>();
d_at_f1_1 = k_at_f1_1.template view<DeviceType>();
d_at_f2_1 = k_at_f2_1.template view<DeviceType>();
d_at_f3_1 = k_at_f3_1.template view<DeviceType>();
d_at_f1_2 = k_at_f1_2.template view<DeviceType>();
d_at_f2_2 = k_at_f2_2.template view<DeviceType>();
d_at_f3_2 = k_at_f3_2.template view<DeviceType>();
d_at_theta0_1 = k_at_theta0_1.template view<DeviceType>();
d_at_theta0_2 = k_at_theta0_2.template view<DeviceType>();
d_aat_k = k_aat_k.template view<DeviceType>();
d_aat_theta0_1 = k_aat_theta0_1.template view<DeviceType>();
d_aat_theta0_2 = k_aat_theta0_2.template view<DeviceType>();
d_bb13t_k = k_bb13t_k.template view<DeviceType>();
d_bb13t_r10 = k_bb13t_r10.template view<DeviceType>();
d_bb13t_r30 = k_bb13t_r30.template view<DeviceType>();
d_setflag_d = k_setflag_d.template view<DeviceType>();
d_setflag_mbt = k_setflag_mbt.template view<DeviceType>();
d_setflag_ebt = k_setflag_ebt.template view<DeviceType>();
d_setflag_at = k_setflag_at.template view<DeviceType>();
d_setflag_aat = k_setflag_aat.template view<DeviceType>();
d_setflag_bb13t = k_setflag_bb13t.template view<DeviceType>();
for (int i = 1; i <= n; i++) {
k_k1.h_view[i] = k1[i];
k_k2.h_view[i] = k2[i];
k_k3.h_view[i] = k3[i];
k_phi1.h_view[i] = phi1[i];
k_phi2.h_view[i] = phi2[i];
k_phi3.h_view[i] = phi3[i];
k_mbt_f1.h_view[i] = mbt_f1[i];
k_mbt_f2.h_view[i] = mbt_f2[i];
k_mbt_f3.h_view[i] = mbt_f3[i];
k_mbt_r0.h_view[i] = mbt_r0[i];
k_ebt_f1_1.h_view[i] = ebt_f1_1[i];
k_ebt_f2_1.h_view[i] = ebt_f2_1[i];
k_ebt_f3_1.h_view[i] = ebt_f3_1[i];
k_ebt_r0_1.h_view[i] = ebt_r0_1[i];
k_ebt_f1_2.h_view[i] = ebt_f1_2[i];
k_ebt_f2_2.h_view[i] = ebt_f2_2[i];
k_ebt_f3_2.h_view[i] = ebt_f3_2[i];
k_ebt_r0_2.h_view[i] = ebt_r0_2[i];
k_at_f1_1.h_view[i] = at_f1_1[i];
k_at_f2_1.h_view[i] = at_f2_1[i];
k_at_f3_1.h_view[i] = at_f3_1[i];
k_at_f1_2.h_view[i] = at_f1_2[i];
k_at_f2_2.h_view[i] = at_f2_2[i];
k_at_f3_2.h_view[i] = at_f3_2[i];
k_at_theta0_1.h_view[i] = at_theta0_1[i];
k_at_theta0_2.h_view[i] = at_theta0_2[i];
k_aat_k.h_view[i] = aat_k[i];
k_aat_theta0_1.h_view[i] = aat_theta0_1[i];
k_aat_theta0_2.h_view[i] = aat_theta0_2[i];
k_bb13t_k.h_view[i] = bb13t_k[i];
k_bb13t_r10.h_view[i] = bb13t_r10[i];
k_bb13t_r30.h_view[i] = bb13t_r30[i];
k_setflag_d.h_view[i] = setflag_d[i];
k_setflag_mbt.h_view[i] = setflag_mbt[i];
k_setflag_ebt.h_view[i] = setflag_ebt[i];
k_setflag_at.h_view[i] = setflag_at[i];
k_setflag_aat.h_view[i] = setflag_aat[i];
k_setflag_bb13t.h_view[i] = setflag_bb13t[i];
}
k_k1.template modify<LMPHostType>();
k_k2.template modify<LMPHostType>();
k_k3.template modify<LMPHostType>();
k_phi1.template modify<LMPHostType>();
k_phi2.template modify<LMPHostType>();
k_phi3.template modify<LMPHostType>();
k_mbt_f1.template modify<LMPHostType>();
k_mbt_f2.template modify<LMPHostType>();
k_mbt_f3.template modify<LMPHostType>();
k_mbt_r0.template modify<LMPHostType>();
k_ebt_f1_1.template modify<LMPHostType>();
k_ebt_f2_1.template modify<LMPHostType>();
k_ebt_f3_1.template modify<LMPHostType>();
k_ebt_r0_1.template modify<LMPHostType>();
k_ebt_f1_2.template modify<LMPHostType>();
k_ebt_f2_2.template modify<LMPHostType>();
k_ebt_f3_2.template modify<LMPHostType>();
k_ebt_r0_2.template modify<LMPHostType>();
k_at_f1_1.template modify<LMPHostType>();
k_at_f2_1.template modify<LMPHostType>();
k_at_f3_1.template modify<LMPHostType>();
k_at_f1_2.template modify<LMPHostType>();
k_at_f2_2.template modify<LMPHostType>();
k_at_f3_2.template modify<LMPHostType>();
k_at_theta0_1.template modify<LMPHostType>();
k_at_theta0_2.template modify<LMPHostType>();
k_aat_k.template modify<LMPHostType>();
k_aat_theta0_1.template modify<LMPHostType>();
k_aat_theta0_2.template modify<LMPHostType>();
k_bb13t_k.template modify<LMPHostType>();
k_bb13t_r10.template modify<LMPHostType>();
k_bb13t_r30.template modify<LMPHostType>();
k_setflag_d.template modify<LMPHostType>();
k_setflag_mbt.template modify<LMPHostType>();
k_setflag_ebt.template modify<LMPHostType>();
k_setflag_at.template modify<LMPHostType>();
k_setflag_aat.template modify<LMPHostType>();
k_setflag_bb13t.template modify<LMPHostType>();
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
= vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
template<class DeviceType>
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void DihedralClass2Kokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i1, const int i2, const int i3, const int i4,
F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4,
const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z,
const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z,
const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const
{
E_FLOAT edihedralquarter;
F_FLOAT v[6];
// The eatom and vatom arrays are atomic
Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_eatom = k_eatom.view<DeviceType>();
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_vatom = k_vatom.view<DeviceType>();
if (eflag_either) {
if (eflag_global) {
if (newton_bond) ev.evdwl += edihedral;
else {
edihedralquarter = 0.25*edihedral;
if (i1 < nlocal) ev.evdwl += edihedralquarter;
if (i2 < nlocal) ev.evdwl += edihedralquarter;
if (i3 < nlocal) ev.evdwl += edihedralquarter;
if (i4 < nlocal) ev.evdwl += edihedralquarter;
}
}
if (eflag_atom) {
edihedralquarter = 0.25*edihedral;
if (newton_bond || i1 < nlocal) v_eatom[i1] += edihedralquarter;
if (newton_bond || i2 < nlocal) v_eatom[i2] += edihedralquarter;
if (newton_bond || i3 < nlocal) v_eatom[i3] += edihedralquarter;
if (newton_bond || i4 < nlocal) v_eatom[i4] += edihedralquarter;
}
}
if (vflag_either) {
v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0];
v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1];
v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2];
v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1];
v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2];
v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2];
if (vflag_global) {
if (newton_bond) {
ev.v[0] += v[0];
ev.v[1] += v[1];
ev.v[2] += v[2];
ev.v[3] += v[3];
ev.v[4] += v[4];
ev.v[5] += v[5];
} else {
if (i1 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
if (i2 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
if (i3 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
if (i4 < nlocal) {
ev.v[0] += 0.25*v[0];
ev.v[1] += 0.25*v[1];
ev.v[2] += 0.25*v[2];
ev.v[3] += 0.25*v[3];
ev.v[4] += 0.25*v[4];
ev.v[5] += 0.25*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i1 < nlocal) {
v_vatom(i1,0) += 0.25*v[0];
v_vatom(i1,1) += 0.25*v[1];
v_vatom(i1,2) += 0.25*v[2];
v_vatom(i1,3) += 0.25*v[3];
v_vatom(i1,4) += 0.25*v[4];
v_vatom(i1,5) += 0.25*v[5];
}
if (newton_bond || i2 < nlocal) {
v_vatom(i2,0) += 0.25*v[0];
v_vatom(i2,1) += 0.25*v[1];
v_vatom(i2,2) += 0.25*v[2];
v_vatom(i2,3) += 0.25*v[3];
v_vatom(i2,4) += 0.25*v[4];
v_vatom(i2,5) += 0.25*v[5];
}
if (newton_bond || i3 < nlocal) {
v_vatom(i3,0) += 0.25*v[0];
v_vatom(i3,1) += 0.25*v[1];
v_vatom(i3,2) += 0.25*v[2];
v_vatom(i3,3) += 0.25*v[3];
v_vatom(i3,4) += 0.25*v[4];
v_vatom(i3,5) += 0.25*v[5];
}
if (newton_bond || i4 < nlocal) {
v_vatom(i4,0) += 0.25*v[0];
v_vatom(i4,1) += 0.25*v[1];
v_vatom(i4,2) += 0.25*v[2];
v_vatom(i4,3) += 0.25*v[3];
v_vatom(i4,4) += 0.25*v[4];
v_vatom(i4,5) += 0.25*v[5];
}
}
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class DihedralClass2Kokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class DihedralClass2Kokkos<LMPHostType>;
#endif
}
c4science · Help