/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator Original Version: http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- USER-CUDA Package and associated modifications: https://sourceforge.net/projects/lammpscuda/ Christian Trott, christian.trott@tu-ilmenau.de Lars Winterfeld, lars.winterfeld@tu-ilmenau.de Theoretical Physics II, University of Technology Ilmenau, Germany See the README file in the USER-CUDA directory. This software is distributed under the GNU General Public License. ------------------------------------------------------------------------- */ __device__ void v_tally(int& vflag_global,int& vflag_atom,int& n, int *list, ENERGY_FLOAT total, ENERGY_FLOAT *v) { /*if(vflag_global) { ENERGY_FLOAT fraction = n/total; ENERGY_FLOAT* shared = &sharedmem[threadIdx.x]; *shared += fraction*v[0]; shared+=blockDim.x; *shared += fraction*v[1]; shared+=blockDim.x; *shared += fraction*v[2]; shared+=blockDim.x; *shared += fraction*v[3]; shared+=blockDim.x; *shared += fraction*v[4]; shared+=blockDim.x; *shared += fraction*v[5]; }*/ if (vflag_atom) { ENERGY_FLOAT fraction = ENERGY_F(1.0)/total; for (int i = 0; i < n; i++) { int m = list[i]; ENERGY_FLOAT* myvatom=&_vatom[m]; *myvatom += fraction*v[0]; myvatom+=_nmax; *myvatom += fraction*v[1]; myvatom+=_nmax; *myvatom += fraction*v[2]; myvatom+=_nmax; *myvatom += fraction*v[3]; myvatom+=_nmax; *myvatom += fraction*v[4]; myvatom+=_nmax; *myvatom += fraction*v[5]; } } } inline __device__ void minimum_image(X_FLOAT3& delta) { if (_triclinic == 0) { if (_periodicity[0]) { delta.x += delta.x < -X_F(0.5)*_prd[0] ? _prd[0] : (delta.x > X_F(0.5)*_prd[0] ?-_prd[0] : X_F(0.0)); } if (_periodicity[1]) { delta.y += delta.y < -X_F(0.5)*_prd[1] ? _prd[1] : (delta.y > X_F(0.5)*_prd[1] ?-_prd[1] : X_F(0.0)); } if (_periodicity[2]) { delta.z += delta.z < -X_F(0.5)*_prd[2] ? _prd[2] : (delta.z > X_F(0.5)*_prd[2] ?-_prd[2] : X_F(0.0)); } } else { if (_periodicity[1]) { delta.z += delta.z < -X_F(0.5)*_prd[2] ? _prd[2] : (delta.z > X_F(0.5)*_prd[2] ?-_prd[2] : X_F(0.0)); delta.y += delta.z < -X_F(0.5)*_prd[2] ? _h[3] : (delta.z > X_F(0.5)*_prd[2] ?-_h[3] : X_F(0.0)); delta.x += delta.z < -X_F(0.5)*_prd[2] ? _h[4] : (delta.z > X_F(0.5)*_prd[2] ?-_h[4] : X_F(0.0)); } if (_periodicity[1]) { delta.y += delta.y < -X_F(0.5)*_prd[1] ? _prd[1] : (delta.y > X_F(0.5)*_prd[1] ?-_prd[1] : X_F(0.0)); delta.x += delta.y < -X_F(0.5)*_prd[1] ? _h[5] : (delta.y > X_F(0.5)*_prd[1] ?-_h[5] : X_F(0.0)); } if (_periodicity[0]) { delta.x += delta.x < -X_F(0.5)*_prd[0] ? _prd[0] : (delta.x > X_F(0.5)*_prd[0] ?-_prd[0] : X_F(0.0)); } } } __global__ void FixShakeCuda_UnconstrainedUpdate_Kernel() { int i=(blockIdx.x*gridDim.y+blockIdx.y)*blockDim.x+threadIdx.x; if(i>=_nlocal) return; X_FLOAT3 my_xshake = {X_F(0.0),X_F(0.0),X_F(0.0)}; if(_shake_flag[i]) { F_FLOAT* my_f = _f + i; V_FLOAT* my_v = _v + i; X_FLOAT* my_x = _x + i; V_FLOAT dtfmsq = _dtfsq; if(_rmass_flag) dtfmsq*= V_F(1.0) / _rmass[i]; else dtfmsq*= V_F(1.0) / _mass[_type[i]]; my_xshake.x = *my_x + _dtv* *my_v + dtfmsq* *my_f; my_f += _nmax; my_v += _nmax; my_x += _nmax; my_xshake.y = *my_x + _dtv* *my_v + dtfmsq* *my_f; my_f += _nmax; my_v += _nmax; my_x += _nmax; my_xshake.z = *my_x + _dtv* *my_v + dtfmsq* *my_f; } _xshake[i]=my_xshake; } __device__ void FixShakeCuda_Shake2(int& vflag,int& vflag_atom,int& m) { int nlist,list[2]; ENERGY_FLOAT v[6]; X_FLOAT invmass0,invmass1; // local atom IDs and constraint distances int i0 = _map_array[_shake_atom[m]]; int i1 = _map_array[_shake_atom[m+_nmax]]; X_FLOAT bond1 = _bond_distance[_shake_type[m]]; // r01 = distance vec between atoms, with PBC X_FLOAT3 r01; X_FLOAT4 x_i0,x_i1; x_i0=fetchXType(i0); x_i1=fetchXType(i1); r01.x = x_i0.x - x_i1.x; r01.y = x_i0.y - x_i1.y; r01.z = x_i0.z - x_i1.z; minimum_image(r01); // s01 = distance vec after unconstrained update, with PBC X_FLOAT3 s01; X_FLOAT3 xs_i0=_xshake[i0]; X_FLOAT3 xs_i1=_xshake[i1]; s01.x = xs_i0.x - xs_i1.x; s01.y = xs_i0.y - xs_i1.y; s01.z = xs_i0.z - xs_i1.z; minimum_image(s01); // scalar distances between atoms X_FLOAT r01sq = r01.x*r01.x + r01.y*r01.y + r01.z*r01.z; X_FLOAT s01sq = s01.x*s01.x + s01.y*s01.y + s01.z*s01.z; // a,b,c = coeffs in quadratic equation for lamda if (_rmass_flag) { invmass0 = X_F(1.0)/_rmass[i0]; invmass1 = X_F(1.0)/_rmass[i1]; } else { invmass0 = X_F(1.0)/_mass[static_cast (x_i0.w)]; invmass1 = X_F(1.0)/_mass[static_cast (x_i1.w)]; } X_FLOAT a = (invmass0+invmass1)*(invmass0+invmass1) * r01sq; X_FLOAT b = X_F(2.0) * (invmass0+invmass1) * (s01.x*r01.x + s01.y*r01.y + s01.z*r01.z); X_FLOAT c = s01sq - bond1*bond1; // error check X_FLOAT determ = b*b - X_F(4.0)*a*c; if (determ < X_F(0.0)) { _flag[0]++; determ = X_F(0.0); } // exact quadratic solution for lamda X_FLOAT lamda,lamda1,lamda2; lamda1 = -b+_SQRT_(determ); lamda2 = -lamda1 - X_F(2.0)*b; lamda1 *= X_F(1.0) / (X_F(2.0)*a); lamda2 *= X_F(1.0) / (X_F(2.0)*a); lamda = (fabs(lamda1) <= fabs(lamda2))? lamda1 : lamda2; // update forces if atom is owned by this processor lamda*= X_F(1.0)/_dtfsq; //attenion: are shake clusters <-> atom unique? nlist = 0; if (i0 < _nlocal) { _f[i0] += lamda*r01.x; _f[i0+_nmax] += lamda*r01.y; _f[i0+2*_nmax] += lamda*r01.z; list[nlist++] = i0; } if (i1 < _nlocal) { _f[i1] -= lamda*r01.x; _f[i1+_nmax] -= lamda*r01.y; _f[i1+2*_nmax] -= lamda*r01.z; list[nlist++] = i1; } if (vflag||vflag_atom) { ENERGY_FLOAT* shared = &sharedmem[threadIdx.x]; X_FLOAT factor=nlist; v[0] = lamda*r01.x*r01.x; *shared = factor*v[0]; shared+=blockDim.x; //times 2.0 since the reducing function is the same as in force calculations, which adds a factor 0.5 v[1] = lamda*r01.y*r01.y; *shared = factor*v[1]; shared+=blockDim.x; v[2] = lamda*r01.z*r01.z; *shared = factor*v[2]; shared+=blockDim.x; v[3] = lamda*r01.x*r01.y; *shared = factor*v[3]; shared+=blockDim.x; v[4] = lamda*r01.x*r01.z; *shared = factor*v[4]; shared+=blockDim.x; v[5] = lamda*r01.y*r01.z; *shared = factor*v[5]; shared+=blockDim.x; v_tally(vflag,vflag_atom,nlist,list,2.0,v); } } __device__ void FixShakeCuda_Shake3(int& vflag,int& vflag_atom,int& m) { int nlist,list[3]; ENERGY_FLOAT v[6]; X_FLOAT invmass0,invmass1,invmass2; // local atom IDs and constraint distances int i0 = _map_array[_shake_atom[m]]; int i1 = _map_array[_shake_atom[m+_nmax]]; int i2 = _map_array[_shake_atom[m+2*_nmax]]; X_FLOAT bond1 = _bond_distance[_shake_type[m]]; X_FLOAT bond2 = _bond_distance[_shake_type[m+_nmax]]; // r01 = distance vec between atoms, with PBC X_FLOAT3 r01,r02; X_FLOAT4 x_i0,x_i1,x_i2; x_i0=fetchXType(i0); x_i1=fetchXType(i1); x_i2=fetchXType(i2); r01.x = x_i0.x - x_i1.x; r01.y = x_i0.y - x_i1.y; r01.z = x_i0.z - x_i1.z; minimum_image(r01); r02.x = x_i0.x - x_i2.x; r02.y = x_i0.y - x_i2.y; r02.z = x_i0.z - x_i2.z; minimum_image(r02); // s01 = distance vec after unconstrained update, with PBC X_FLOAT3 s01,s02; X_FLOAT3 xs_i0=_xshake[i0]; X_FLOAT3 xs_i1=_xshake[i1]; X_FLOAT3 xs_i2=_xshake[i2]; s01.x = xs_i0.x - xs_i1.x; s01.y = xs_i0.y - xs_i1.y; s01.z = xs_i0.z - xs_i1.z; minimum_image(s01); s02.x = xs_i0.x - xs_i2.x; s02.y = xs_i0.y - xs_i2.y; s02.z = xs_i0.z - xs_i2.z; minimum_image(s02); // scalar distances between atoms X_FLOAT r01sq = r01.x*r01.x + r01.y*r01.y + r01.z*r01.z; X_FLOAT r02sq = r02.x*r02.x + r02.y*r02.y + r02.z*r02.z; X_FLOAT s01sq = s01.x*s01.x + s01.y*s01.y + s01.z*s01.z; X_FLOAT s02sq = s02.x*s02.x + s02.y*s02.y + s02.z*s02.z; // a,b,c = coeffs in quadratic equation for lamda if (_rmass_flag) { invmass0 = X_F(1.0)/_rmass[i0]; invmass1 = X_F(1.0)/_rmass[i1]; invmass2 = X_F(1.0)/_rmass[i2]; } else { invmass0 = X_F(1.0)/_mass[static_cast (x_i0.w)]; invmass1 = X_F(1.0)/_mass[static_cast (x_i1.w)]; invmass2 = X_F(1.0)/_mass[static_cast (x_i2.w)]; } X_FLOAT a11 = X_F(2.0) * (invmass0+invmass1) * (s01.x*r01.x + s01.y*r01.y + s01.z*r01.z); X_FLOAT a12 = X_F(2.0) * invmass0 * (s01.x*r02.x + s01.y*r02.y + s01.z*r02.z); X_FLOAT a21 = X_F(2.0) * invmass0 * (s02.x*r01.x + s02.y*r01.y + s02.z*r01.z); X_FLOAT a22 = X_F(2.0) * (invmass0+invmass2) * (s02.x*r02.x + s02.y*r02.y + s02.z*r02.z); // error check X_FLOAT determ = a11*a22 - a12*a21; if (determ == X_F(0.0)) _flag[0]++; X_FLOAT determinv = X_F(1.0)/determ; X_FLOAT a11inv = a22*determinv; X_FLOAT a12inv = -a12*determinv; X_FLOAT a21inv = -a21*determinv; X_FLOAT a22inv = a11*determinv; // quadratic correction coeffs X_FLOAT r0102 = (r01.x*r02.x + r01.y*r02.y + r01.z*r02.z); X_FLOAT quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq; X_FLOAT quad1_0202 = invmass0*invmass0 * r02sq; X_FLOAT quad1_0102 = X_F(2.0) * (invmass0+invmass1)*invmass0 * r0102; X_FLOAT quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq; X_FLOAT quad2_0101 = invmass0*invmass0 * r01sq; X_FLOAT quad2_0102 = X_F(2.0) * (invmass0+invmass2)*invmass0 * r0102; // iterate until converged X_FLOAT lamda01 = X_F(0.0); X_FLOAT lamda02 = X_F(0.0); int niter = 0; int done = 0; X_FLOAT quad1,quad2,b1,b2,lamda01_new,lamda02_new; //maybe all running full loop? while (__any(!done) && niter < _max_iter) { quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 + quad1_0102 * lamda01*lamda02; quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 + quad2_0102 * lamda01*lamda02; b1 = bond1*bond1 - s01sq - quad1; b2 = bond2*bond2 - s02sq - quad2; lamda01_new = a11inv*b1 + a12inv*b2; lamda02_new = a21inv*b1 + a22inv*b2; done++; done = (fabs(lamda01_new-lamda01) > _tolerance)?0: done; done = (fabs(lamda02_new-lamda02) > _tolerance)?0: done; lamda01 = done<2?lamda01_new:lamda01; lamda02 = done<2?lamda02_new:lamda02; niter++; } // update forces if atom is owned by this processor lamda01 *= X_F(1.0)/_dtfsq; lamda02 *= X_F(1.0)/_dtfsq; //attenion: are shake clusters <-> atom unique? nlist = 0; if (i0 < _nlocal) { _f[i0] += lamda01*r01.x + lamda02*r02.x; _f[i0+_nmax] += lamda01*r01.y + lamda02*r02.y; _f[i0+2*_nmax] += lamda01*r01.z + lamda02*r02.z; list[nlist++] = i0; } if (i1 < _nlocal) { _f[i1] -= lamda01*r01.x; _f[i1+_nmax] -= lamda01*r01.y; _f[i1+2*_nmax] -= lamda01*r01.z; list[nlist++] = i1; } if (i2 < _nlocal) { _f[i2] -= lamda02*r02.x; _f[i2+_nmax] -= lamda02*r02.y; _f[i2+2*_nmax] -= lamda02*r02.z; list[nlist++] = i2; } if (vflag||vflag_atom) { ENERGY_FLOAT* shared = &sharedmem[threadIdx.x]; X_FLOAT factor=X_F(2.0)/X_F(3.0)*nlist; v[0] = lamda01*r01.x*r01.x + lamda02*r02.x*r02.x; *shared = factor*v[0]; shared+=blockDim.x; //times 2.0 since the reducing function is the same as in force calculations, which adds a factor 0.5 v[1] = lamda01*r01.y*r01.y + lamda02*r02.y*r02.y; *shared = factor*v[1]; shared+=blockDim.x; v[2] = lamda01*r01.z*r01.z + lamda02*r02.z*r02.z; *shared = factor*v[2]; shared+=blockDim.x; v[3] = lamda01*r01.x*r01.y + lamda02*r02.x*r02.y; *shared = factor*v[3]; shared+=blockDim.x; v[4] = lamda01*r01.x*r01.z + lamda02*r02.x*r02.z; *shared = factor*v[4]; shared+=blockDim.x; v[5] = lamda01*r01.y*r01.z + lamda02*r02.y*r02.z; *shared = factor*v[5]; shared+=blockDim.x; v_tally(vflag,vflag_atom,nlist,list,3.0,v); } } __device__ void FixShakeCuda_Shake4(int& vflag,int& vflag_atom,int& m) { int nlist,list[4]; ENERGY_FLOAT v[6]; X_FLOAT invmass0,invmass1,invmass2,invmass3; // local atom IDs and constraint distances int i0 = _map_array[_shake_atom[m]]; int i1 = _map_array[_shake_atom[m+_nmax]]; int i2 = _map_array[_shake_atom[m+2*_nmax]]; int i3 = _map_array[_shake_atom[m+3*_nmax]]; X_FLOAT bond1 = _bond_distance[_shake_type[m]]; X_FLOAT bond2 = _bond_distance[_shake_type[m+_nmax]]; X_FLOAT bond3 = _bond_distance[_shake_type[m+2*_nmax]]; // r01 = distance vec between atoms, with PBC X_FLOAT3 r01,r02,r03; X_FLOAT4 x_i0,x_i1,x_i2,x_i3; x_i0=fetchXType(i0); x_i1=fetchXType(i1); x_i2=fetchXType(i2); x_i3=fetchXType(i3); r01.x = x_i0.x - x_i1.x; r01.y = x_i0.y - x_i1.y; r01.z = x_i0.z - x_i1.z; minimum_image(r01); r02.x = x_i0.x - x_i2.x; r02.y = x_i0.y - x_i2.y; r02.z = x_i0.z - x_i2.z; minimum_image(r02); r03.x = x_i0.x - x_i3.x; r03.y = x_i0.y - x_i3.y; r03.z = x_i0.z - x_i3.z; minimum_image(r03); // s01 = distance vec after unconstrained update, with PBC X_FLOAT3 s01,s02,s03; X_FLOAT3 xs_i0=_xshake[i0]; X_FLOAT3 xs_i1=_xshake[i1]; X_FLOAT3 xs_i2=_xshake[i2]; X_FLOAT3 xs_i3=_xshake[i3]; s01.x = xs_i0.x - xs_i1.x; s01.y = xs_i0.y - xs_i1.y; s01.z = xs_i0.z - xs_i1.z; minimum_image(s01); s02.x = xs_i0.x - xs_i2.x; s02.y = xs_i0.y - xs_i2.y; s02.z = xs_i0.z - xs_i2.z; minimum_image(s02); s03.x = xs_i0.x - xs_i3.x; s03.y = xs_i0.y - xs_i3.y; s03.z = xs_i0.z - xs_i3.z; minimum_image(s03); // scalar distances between atoms X_FLOAT r01sq = r01.x*r01.x + r01.y*r01.y + r01.z*r01.z; X_FLOAT r02sq = r02.x*r02.x + r02.y*r02.y + r02.z*r02.z; X_FLOAT r03sq = r03.x*r03.x + r03.y*r03.y + r03.z*r03.z; X_FLOAT s01sq = s01.x*s01.x + s01.y*s01.y + s01.z*s01.z; X_FLOAT s02sq = s02.x*s02.x + s02.y*s02.y + s02.z*s02.z; X_FLOAT s03sq = s03.x*s03.x + s03.y*s03.y + s03.z*s03.z; // a,b,c = coeffs in quadratic equation for lamda if (_rmass_flag) { invmass0 = X_F(1.0)/_rmass[i0]; invmass1 = X_F(1.0)/_rmass[i1]; invmass2 = X_F(1.0)/_rmass[i2]; invmass3 = X_F(1.0)/_rmass[i3]; } else { invmass0 = X_F(1.0)/_mass[static_cast (x_i0.w)]; invmass1 = X_F(1.0)/_mass[static_cast (x_i1.w)]; invmass2 = X_F(1.0)/_mass[static_cast (x_i2.w)]; invmass3 = X_F(1.0)/_mass[static_cast (x_i3.w)]; } X_FLOAT a11 = X_F(2.0) * (invmass0+invmass1) * (s01.x*r01.x + s01.y*r01.y + s01.z*r01.z); X_FLOAT a12 = X_F(2.0) * invmass0 * (s01.x*r02.x + s01.y*r02.y + s01.z*r02.z); X_FLOAT a13 = X_F(2.0) * invmass0 * (s01.x*r03.x + s01.y*r03.y + s01.z*r03.z); X_FLOAT a21 = X_F(2.0) * invmass0 * (s02.x*r01.x + s02.y*r01.y + s02.z*r01.z); X_FLOAT a22 = X_F(2.0) * (invmass0+invmass2) * (s02.x*r02.x + s02.y*r02.y + s02.z*r02.z); X_FLOAT a23 = X_F(2.0) * (invmass0) * (s02.x*r03.x + s02.y*r03.y + s02.z*r03.z); X_FLOAT a31 = X_F(2.0) * (invmass0) * (s03.x*r01.x + s03.y*r01.y + s03.z*r01.z); X_FLOAT a32 = X_F(2.0) * (invmass0) * (s03.x*r02.x + s03.y*r02.y + s03.z*r02.z); X_FLOAT a33 = X_F(2.0) * (invmass0+invmass3) * (s03.x*r03.x + s03.y*r03.y + s03.z*r03.z); // error check X_FLOAT determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 - a11*a23*a32 - a12*a21*a33 - a13*a22*a31; if (determ == X_F(0.0)) _flag[0]++; X_FLOAT determinv = X_F(1.0)/determ; X_FLOAT a11inv = determinv * (a22*a33 - a23*a32); X_FLOAT a12inv = -determinv * (a12*a33 - a13*a32); X_FLOAT a13inv = determinv * (a12*a23 - a13*a22); X_FLOAT a21inv = -determinv * (a21*a33 - a23*a31); X_FLOAT a22inv = determinv * (a11*a33 - a13*a31); X_FLOAT a23inv = -determinv * (a11*a23 - a13*a21); X_FLOAT a31inv = determinv * (a21*a32 - a22*a31); X_FLOAT a32inv = -determinv * (a11*a32 - a12*a31); X_FLOAT a33inv = determinv * (a11*a22 - a12*a21); // quadratic correction coeffs X_FLOAT r0102 = (r01.x*r02.x + r01.y*r02.y + r01.z*r02.z); X_FLOAT r0103 = (r01.x*r03.x + r01.y*r03.y + r01.z*r03.z); X_FLOAT r0203 = (r02.x*r03.x + r02.y*r03.y + r02.z*r03.z); X_FLOAT quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq; X_FLOAT quad1_0202 = invmass0*invmass0 * r02sq; X_FLOAT quad1_0303 = invmass0*invmass0 * r03sq; X_FLOAT quad1_0102 = X_F(2.0) * (invmass0+invmass1)*invmass0 * r0102; X_FLOAT quad1_0103 = X_F(2.0) * (invmass0+invmass1)*invmass0 * r0103; X_FLOAT quad1_0203 = X_F(2.0) * invmass0*invmass0 * r0203; X_FLOAT quad2_0101 = invmass0*invmass0 * r01sq; X_FLOAT quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq; X_FLOAT quad2_0303 = invmass0*invmass0 * r03sq; X_FLOAT quad2_0102 = X_F(2.0) * (invmass0+invmass2)*invmass0 * r0102; X_FLOAT quad2_0103 = X_F(2.0) * invmass0*invmass0 * r0103; X_FLOAT quad2_0203 = X_F(2.0) * (invmass0+invmass2)*invmass0 * r0203; X_FLOAT quad3_0101 = invmass0*invmass0 * r01sq; X_FLOAT quad3_0202 = invmass0*invmass0 * r02sq; X_FLOAT quad3_0303 = (invmass0+invmass3)*(invmass0+invmass3) * r03sq; X_FLOAT quad3_0102 = X_F(2.0) * invmass0*invmass0 * r0102; X_FLOAT quad3_0103 = X_F(2.0) * (invmass0+invmass3)*invmass0 * r0103; X_FLOAT quad3_0203 = X_F(2.0) * (invmass0+invmass3)*invmass0 * r0203; // iterate until converged X_FLOAT lamda01 = X_F(0.0); X_FLOAT lamda02 = X_F(0.0); X_FLOAT lamda03 = X_F(0.0); int niter = 0; int done = 0; X_FLOAT quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda03_new; //maybe all running full loop? while (__any(!done) && niter < _max_iter) { quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 + quad1_0303 * lamda03*lamda03 + quad1_0102 * lamda01*lamda02 + quad1_0103 * lamda01*lamda03 + quad1_0203 * lamda02*lamda03; quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 + quad2_0303 * lamda03*lamda03 + quad2_0102 * lamda01*lamda02 + quad2_0103 * lamda01*lamda03 + quad2_0203 * lamda02*lamda03; quad3 = quad3_0101 * lamda01*lamda01 + quad3_0202 * lamda02*lamda02 + quad3_0303 * lamda03*lamda03 + quad3_0102 * lamda01*lamda02 + quad3_0103 * lamda01*lamda03 + quad3_0203 * lamda02*lamda03; b1 = bond1*bond1 - s01sq - quad1; b2 = bond2*bond2 - s02sq - quad2; b3 = bond3*bond3 - s03sq - quad3; lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3; lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3; lamda03_new = a31inv*b1 + a32inv*b2 + a33inv*b3; done++; done = (fabs(lamda01_new-lamda01) > _tolerance)? 0:done; done = (fabs(lamda02_new-lamda02) > _tolerance)? 0:done; done = (fabs(lamda03_new-lamda03) > _tolerance)? 0:done; lamda01 = done<2?lamda01_new:lamda01; lamda02 = done<2?lamda02_new:lamda02; lamda03 = done<2?lamda03_new:lamda03; niter++; } // update forces if atom is owned by this processor lamda01 *= X_F(1.0)/_dtfsq; lamda02 *= X_F(1.0)/_dtfsq; lamda03 *= X_F(1.0)/_dtfsq; //attenion: are shake clusters <-> atom unique? nlist = 0; if (i0 < _nlocal) { _f[i0] += lamda01*r01.x + lamda02*r02.x + lamda03*r03.x; _f[i0+_nmax] += lamda01*r01.y + lamda02*r02.y + lamda03*r03.y; _f[i0+2*_nmax] += lamda01*r01.z + lamda02*r02.z + lamda03*r03.z; list[nlist++] = i0; } if (i1 < _nlocal) { _f[i1] -= lamda01*r01.x; _f[i1+_nmax] -= lamda01*r01.y; _f[i1+2*_nmax] -= lamda01*r01.z; list[nlist++] = i1; } if (i2 < _nlocal) { _f[i2] -= lamda02*r02.x; _f[i2+_nmax] -= lamda02*r02.y; _f[i2+2*_nmax] -= lamda02*r02.z; list[nlist++] = i2; } if (i3 < _nlocal) { _f[i3] -= lamda03*r03.x; _f[i3+_nmax] -= lamda03*r03.y; _f[i3+2*_nmax] -= lamda03*r03.z; list[nlist++] = i3; } if (vflag||vflag_atom) { ENERGY_FLOAT* shared = &sharedmem[threadIdx.x]; X_FLOAT factor=X_F(2.0)/X_F(4.0)*nlist; v[0] = lamda01*r01.x*r01.x + lamda02*r02.x*r02.x + lamda03*r03.x*r03.x; *shared = factor*v[0]; shared+=blockDim.x; //times 2.0 since the reducing function is the same as in force calculations, which adds a factor 0.5 v[1] = lamda01*r01.y*r01.y + lamda02*r02.y*r02.y + lamda03*r03.y*r03.y; *shared = factor*v[1]; shared+=blockDim.x; v[2] = lamda01*r01.z*r01.z + lamda02*r02.z*r02.z + lamda03*r03.z*r03.z; *shared = factor*v[2]; shared+=blockDim.x; v[3] = lamda01*r01.x*r01.y + lamda02*r02.x*r02.y + lamda03*r03.x*r03.y; *shared = factor*v[3]; shared+=blockDim.x; v[4] = lamda01*r01.x*r01.z + lamda02*r02.x*r02.z + lamda03*r03.x*r03.z; *shared = factor*v[4]; shared+=blockDim.x; v[5] = lamda01*r01.y*r01.z + lamda02*r02.y*r02.z + lamda03*r03.y*r03.z; *shared = factor*v[5]; shared+=blockDim.x; v_tally(vflag,vflag_atom,nlist,list,4.0,v); } } __device__ void FixShakeCuda_Shake3Angle(int& vflag,int& vflag_atom,int& m) { int nlist,list[3]; ENERGY_FLOAT v[6]; X_FLOAT invmass0,invmass1,invmass2; // local atom IDs and constraint distances int i0 = _map_array[_shake_atom[m]]; int i1 = _map_array[_shake_atom[m+_nmax]]; int i2 = _map_array[_shake_atom[m+2*_nmax]]; X_FLOAT bond1 = _bond_distance[_shake_type[m]]; X_FLOAT bond2 = _bond_distance[_shake_type[m+_nmax]]; X_FLOAT bond12 = _angle_distance[_shake_type[m+2*_nmax]]; // r01 = distance vec between atoms, with PBC X_FLOAT3 r01,r02,r12; X_FLOAT4 x_i0,x_i1,x_i2; x_i0=fetchXType(i0); x_i1=fetchXType(i1); x_i2=fetchXType(i2); r01.x = x_i0.x - x_i1.x; r01.y = x_i0.y - x_i1.y; r01.z = x_i0.z - x_i1.z; minimum_image(r01); r02.x = x_i0.x - x_i2.x; r02.y = x_i0.y - x_i2.y; r02.z = x_i0.z - x_i2.z; minimum_image(r02); r12.x = x_i1.x - x_i2.x; r12.y = x_i1.y - x_i2.y; r12.z = x_i1.z - x_i2.z; minimum_image(r12); // s01 = distance vec after unconstrained update, with PBC X_FLOAT3 s01,s02,s12; X_FLOAT3 xs_i0=_xshake[i0]; X_FLOAT3 xs_i1=_xshake[i1]; X_FLOAT3 xs_i2=_xshake[i2]; s01.x = xs_i0.x - xs_i1.x; s01.y = xs_i0.y - xs_i1.y; s01.z = xs_i0.z - xs_i1.z; minimum_image(s01); s02.x = xs_i0.x - xs_i2.x; s02.y = xs_i0.y - xs_i2.y; s02.z = xs_i0.z - xs_i2.z; minimum_image(s02); s12.x = xs_i1.x - xs_i2.x; s12.y = xs_i1.y - xs_i2.y; s12.z = xs_i1.z - xs_i2.z; minimum_image(s12); // scalar distances between atoms X_FLOAT r01sq = r01.x*r01.x + r01.y*r01.y + r01.z*r01.z; X_FLOAT r02sq = r02.x*r02.x + r02.y*r02.y + r02.z*r02.z; X_FLOAT r12sq = r12.x*r12.x + r12.y*r12.y + r12.z*r12.z; X_FLOAT s01sq = s01.x*s01.x + s01.y*s01.y + s01.z*s01.z; X_FLOAT s02sq = s02.x*s02.x + s02.y*s02.y + s02.z*s02.z; X_FLOAT s12sq = s12.x*s12.x + s12.y*s12.y + s12.z*s12.z; // a,b,c = coeffs in quadratic equation for lamda if (_rmass_flag) { invmass0 = X_F(1.0)/_rmass[i0]; invmass1 = X_F(1.0)/_rmass[i1]; invmass2 = X_F(1.0)/_rmass[i2]; } else { invmass0 = X_F(1.0)/_mass[static_cast (x_i0.w)]; invmass1 = X_F(1.0)/_mass[static_cast (x_i1.w)]; invmass2 = X_F(1.0)/_mass[static_cast (x_i2.w)]; } X_FLOAT a11 = X_F(2.0) * (invmass0+invmass1) * (s01.x*r01.x + s01.y*r01.y + s01.z*r01.z); X_FLOAT a12 = X_F(2.0) * invmass0 * (s01.x*r02.x + s01.y*r02.y + s01.z*r02.z); X_FLOAT a13 = - X_F(2.0) * invmass1 * (s01.x*r12.x + s01.y*r12.y + s01.z*r12.z); X_FLOAT a21 = X_F(2.0) * invmass0 * (s02.x*r01.x + s02.y*r01.y + s02.z*r01.z); X_FLOAT a22 = X_F(2.0) * (invmass0+invmass2) * (s02.x*r02.x + s02.y*r02.y + s02.z*r02.z); X_FLOAT a23 = X_F(2.0) * invmass2 * (s02.x*r12.x + s02.y*r12.y + s02.z*r12.z); X_FLOAT a31 = - X_F(2.0) * invmass1 * (s12.x*r01.x + s12.y*r01.y + s12.z*r01.z); X_FLOAT a32 = X_F(2.0) * invmass2 * (s12.x*r02.x + s12.y*r02.y + s12.z*r02.z); X_FLOAT a33 = X_F(2.0) * (invmass1+invmass2) * (s12.x*r12.x + s12.y*r12.y + s12.z*r12.z); // inverse of matrix X_FLOAT determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 - a11*a23*a32 - a12*a21*a33 - a13*a22*a31; if (determ == X_F(0.0)) _flag[0]++; X_FLOAT determinv = X_F(1.0)/determ; X_FLOAT a11inv = determinv * (a22*a33 - a23*a32); X_FLOAT a12inv = -determinv * (a12*a33 - a13*a32); X_FLOAT a13inv = determinv * (a12*a23 - a13*a22); X_FLOAT a21inv = -determinv * (a21*a33 - a23*a31); X_FLOAT a22inv = determinv * (a11*a33 - a13*a31); X_FLOAT a23inv = -determinv * (a11*a23 - a13*a21); X_FLOAT a31inv = determinv * (a21*a32 - a22*a31); X_FLOAT a32inv = -determinv * (a11*a32 - a12*a31); X_FLOAT a33inv = determinv * (a11*a22 - a12*a21); // quadratic correction coeffs X_FLOAT r0102 = (r01.x*r02.x + r01.y*r02.y + r01.z*r02.z); X_FLOAT r0112 = (r01.x*r12.x + r01.y*r12.y + r01.z*r12.z); X_FLOAT r0212 = (r02.x*r12.x + r02.y*r12.y + r02.z*r12.z); X_FLOAT quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq; X_FLOAT quad1_0202 = invmass0*invmass0 * r02sq; X_FLOAT quad1_1212 = invmass1*invmass1 * r12sq; X_FLOAT quad1_0102 = X_F(2.0) * (invmass0+invmass1)*invmass0 * r0102; X_FLOAT quad1_0112 = - X_F(2.0) * (invmass0+invmass1)*invmass1 * r0112; X_FLOAT quad1_0212 = - X_F(2.0) * invmass0*invmass1 * r0212; X_FLOAT quad2_0101 = invmass0*invmass0 * r01sq; X_FLOAT quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq; X_FLOAT quad2_1212 = invmass2*invmass2 * r12sq; X_FLOAT quad2_0102 = X_F(2.0) * (invmass0+invmass2)*invmass0 * r0102; X_FLOAT quad2_0112 = X_F(2.0) * invmass0*invmass2 * r0112; X_FLOAT quad2_0212 = X_F(2.0) * (invmass0+invmass2)*invmass2 * r0212; X_FLOAT quad3_0101 = invmass1*invmass1 * r01sq; X_FLOAT quad3_0202 = invmass2*invmass2 * r02sq; X_FLOAT quad3_1212 = (invmass1+invmass2)*(invmass1+invmass2) * r12sq; X_FLOAT quad3_0102 = - X_F(2.0) * invmass1*invmass2 * r0102; X_FLOAT quad3_0112 = - X_F(2.0) * (invmass1+invmass2)*invmass1 * r0112; X_FLOAT quad3_0212 = X_F(2.0) * (invmass1+invmass2)*invmass2 * r0212; // iterate until converged X_FLOAT lamda01 = X_F(0.0); X_FLOAT lamda02 = X_F(0.0); X_FLOAT lamda12 = X_F(0.0); int niter = 0; int done = 0; X_FLOAT quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new; //maybe all running full loop? while (__any(!done) && niter < _max_iter) { quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 + quad1_1212 * lamda12*lamda12 + quad1_0102 * lamda01*lamda02 + quad1_0112 * lamda01*lamda12 + quad1_0212 * lamda02*lamda12; quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 + quad2_1212 * lamda12*lamda12 + quad2_0102 * lamda01*lamda02 + quad2_0112 * lamda01*lamda12 + quad2_0212 * lamda02*lamda12; quad3 = quad3_0101 * lamda01*lamda01 + quad3_0202 * lamda02*lamda02 + quad3_1212 * lamda12*lamda12 + quad3_0102 * lamda01*lamda02 + quad3_0112 * lamda01*lamda12 + quad3_0212 * lamda02*lamda12; b1 = bond1*bond1 - s01sq - quad1; b2 = bond2*bond2 - s02sq - quad2; b3 = bond12*bond12 - s12sq - quad3; lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3; lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3; lamda12_new = a31inv*b1 + a32inv*b2 + a33inv*b3; done++; done = (fabs(lamda01_new-lamda01) > _tolerance)?0: done; done = (fabs(lamda02_new-lamda02) > _tolerance)?0: done; done = (fabs(lamda12_new-lamda12) > _tolerance)?0: done; lamda01 = done<2?lamda01_new:lamda01; lamda02 = done<2?lamda02_new:lamda02; lamda12 = done<2?lamda12_new:lamda12; niter++; } // update forces if atom is owned by this processor lamda01 *= X_F(1.0)/_dtfsq; lamda02 *= X_F(1.0)/_dtfsq; lamda12 *= X_F(1.0)/_dtfsq; //attenion: are shake clusters <-> atom unique? nlist = 0; if (i0 < _nlocal) { _f[i0] += lamda01*r01.x + lamda02*r02.x; _f[i0+_nmax] += lamda01*r01.y + lamda02*r02.y; _f[i0+2*_nmax] += lamda01*r01.z + lamda02*r02.z; list[nlist++] = i0; } if (i1 < _nlocal) { _f[i1] -= lamda01*r01.x - lamda12*r12.x; _f[i1+_nmax] -= lamda01*r01.y - lamda12*r12.y; _f[i1+2*_nmax] -= lamda01*r01.z - lamda12*r12.z; list[nlist++] = i1; } if (i2 < _nlocal) { _f[i2] -= lamda02*r02.x + lamda12*r12.x; _f[i2+_nmax] -= lamda02*r02.y + lamda12*r12.y; _f[i2+2*_nmax] -= lamda02*r02.z + lamda12*r12.z; list[nlist++] = i2; } if (vflag||vflag_atom) { ENERGY_FLOAT* shared = &sharedmem[threadIdx.x]; X_FLOAT factor=X_F(2.0)/X_F(3.0)*nlist; v[0] = lamda01*r01.x*r01.x + lamda02*r02.x*r02.x + lamda12*r12.x*r12.x; *shared = factor*v[0]; shared+=blockDim.x; //times 2.0 since the reducing function is the same as in force calculations, which adds a factor 0.5 v[1] = lamda01*r01.y*r01.y + lamda02*r02.y*r02.y + lamda12*r12.y*r12.y; *shared = factor*v[1]; shared+=blockDim.x; v[2] = lamda01*r01.z*r01.z + lamda02*r02.z*r02.z + lamda12*r12.z*r12.z; *shared = factor*v[2]; shared+=blockDim.x; v[3] = lamda01*r01.x*r01.y + lamda02*r02.x*r02.y + lamda12*r12.x*r12.y; *shared = factor*v[3]; shared+=blockDim.x; v[4] = lamda01*r01.x*r01.z + lamda02*r02.x*r02.z + lamda12*r12.x*r12.z; *shared = factor*v[4]; shared+=blockDim.x; v[5] = lamda01*r01.y*r01.z + lamda02*r02.y*r02.z + lamda12*r12.y*r12.z; *shared = factor*v[5]; shared+=blockDim.x; v_tally(vflag,vflag_atom,nlist,list,3.0,v); } } __global__ void FixShakeCuda_Shake_Kernel(int vflag,int vflag_atom,int* list,int nlist) { int i=(blockIdx.x*gridDim.y+blockIdx.y)*blockDim.x+threadIdx.x; if(i_nmax) _flag[0]=1; X_FLOAT3 xs=_xshake[j]; ((X_FLOAT*) _buffer)[i]=xs.x + dx; ((X_FLOAT*) _buffer)[i+1*n] = xs.y + dy; ((X_FLOAT*) _buffer)[i+2*n] = xs.z + dz; } } __global__ void FixShakeCuda_PackComm_Self_Kernel(int* sendlist,int n,int maxlistlength,int iswap,X_FLOAT dx,X_FLOAT dy,X_FLOAT dz,int first) { int i=(blockIdx.x*gridDim.y+blockIdx.y)*blockDim.x+threadIdx.x; int* list=sendlist+iswap*maxlistlength; if(i_nmax) _flag[0]=1; X_FLOAT3 xs=_xshake[j]; xs.x += dx; xs.y += dy; xs.z += dz; _xshake[i+first]=xs; } } __global__ void FixShakeCuda_UnpackComm_Kernel(int n,int first) { int i=(blockIdx.x*gridDim.y+blockIdx.y)*blockDim.x+threadIdx.x; if(i