cuda bugfix again
This commit is contained in:
alphataubio
@ -234,6 +234,7 @@ void FixCMAPKokkos<DeviceType>::post_force(int vflag)
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ev_init(eflag,vflag);
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copymode = 1;
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nlocal = atomKK->nlocal;
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Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixCmapPostForce>(0,ncrosstermlist),*this,ecmap);
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copymode = 0;
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atomKK->modified(execution_space,F_MASK);
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@ -245,27 +246,6 @@ template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void FixCMAPKokkos<DeviceType>::operator()(TagFixCmapPostForce, const int n, double &ecmapKK) const
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{
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int i1,i2,i3,i4,i5,type;
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int li1, li2, mli1,mli2,mli11,mli21,t1,li3,li4,mli3,mli4,mli31,mli41;
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// vectors needed to calculate the cross-term dihedral angles
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double vb21x,vb21y,vb21z,vb32x,vb32y,vb32z,vb34x,vb34y,vb34z;
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double vb23x,vb23y,vb23z;
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double vb43x,vb43y,vb43z,vb45x,vb45y,vb45z,a1x,a1y,a1z,b1x,b1y,b1z;
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double a2x,a2y,a2z,b2x,b2y,b2z,r32,a1sq,b1sq,a2sq,b2sq,dpr21r32,dpr34r32;
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double dpr32r43,dpr45r43,r43,vb12x,vb12y,vb12z;
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// cross-term dihedral angles
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double phi,psi,phi1,psi1;
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double f1[3],f2[3],f3[3],f4[3],f5[3];
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double gs[4],d1gs[4],d2gs[4],d12gs[4];
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// vectors needed for the gradient/force calculation
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double dphidr1x,dphidr1y,dphidr1z,dphidr2x,dphidr2y,dphidr2z;
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double dphidr3x,dphidr3y,dphidr3z,dphidr4x,dphidr4y,dphidr4z;
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double dpsidr1x,dpsidr1y,dpsidr1z,dpsidr2x,dpsidr2y,dpsidr2z;
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double dpsidr3x,dpsidr3y,dpsidr3z,dpsidr4x,dpsidr4y,dpsidr4z;
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// Definition of cross-term dihedrals
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// phi dihedral
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@ -275,14 +255,12 @@ void FixCMAPKokkos<DeviceType>::operator()(TagFixCmapPostForce, const int n, dou
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// |--------------------|
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// psi dihedral
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int nlocal = atomKK->nlocal;
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i1 = d_crosstermlist(n,0);
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i2 = d_crosstermlist(n,1);
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i3 = d_crosstermlist(n,2);
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i4 = d_crosstermlist(n,3);
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i5 = d_crosstermlist(n,4);
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type = d_crosstermlist(n,5);
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int i1 = d_crosstermlist(n,0);
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int i2 = d_crosstermlist(n,1);
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int i3 = d_crosstermlist(n,2);
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int i4 = d_crosstermlist(n,3);
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int i5 = d_crosstermlist(n,4);
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int type = d_crosstermlist(n,5);
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if (type == 0) return;
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// calculate bond vectors for both dihedrals
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@ -290,99 +268,103 @@ void FixCMAPKokkos<DeviceType>::operator()(TagFixCmapPostForce, const int n, dou
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// phi
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// vb21 = r2 - r1
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vb21x = d_x(i2,0) - d_x(i1,0);
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vb21y = d_x(i2,1) - d_x(i1,1);
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vb21z = d_x(i2,2) - d_x(i1,2);
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vb12x = -1.0*vb21x;
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vb12y = -1.0*vb21y;
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vb12z = -1.0*vb21z;
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vb32x = d_x(i3,0) - d_x(i2,0);
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vb32y = d_x(i3,1) - d_x(i2,1);
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vb32z = d_x(i3,2) - d_x(i2,2);
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vb23x = -1.0*vb32x;
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vb23y = -1.0*vb32y;
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vb23z = -1.0*vb32z;
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double vb21x = d_x(i2,0) - d_x(i1,0);
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double vb21y = d_x(i2,1) - d_x(i1,1);
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double vb21z = d_x(i2,2) - d_x(i1,2);
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double vb12x = -1.0*vb21x;
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double vb12y = -1.0*vb21y;
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double vb12z = -1.0*vb21z;
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double vb32x = d_x(i3,0) - d_x(i2,0);
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double vb32y = d_x(i3,1) - d_x(i2,1);
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double vb32z = d_x(i3,2) - d_x(i2,2);
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double vb23x = -1.0*vb32x;
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double vb23y = -1.0*vb32y;
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double vb23z = -1.0*vb32z;
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vb34x = d_x(i3,0) - d_x(i4,0);
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vb34y = d_x(i3,1) - d_x(i4,1);
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vb34z = d_x(i3,2) - d_x(i4,2);
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double vb34x = d_x(i3,0) - d_x(i4,0);
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double vb34y = d_x(i3,1) - d_x(i4,1);
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double vb34z = d_x(i3,2) - d_x(i4,2);
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// psi
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// bond vectors same as for phi: vb32
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vb43x = -1.0*vb34x;
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vb43y = -1.0*vb34y;
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vb43z = -1.0*vb34z;
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double vb43x = -1.0*vb34x;
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double vb43y = -1.0*vb34y;
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double vb43z = -1.0*vb34z;
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vb45x = d_x(i4,0) - d_x(i5,0);
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vb45y = d_x(i4,1) - d_x(i5,1);
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vb45z = d_x(i4,2) - d_x(i5,2);
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double vb45x = d_x(i4,0) - d_x(i5,0);
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double vb45y = d_x(i4,1) - d_x(i5,1);
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double vb45z = d_x(i4,2) - d_x(i5,2);
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// calculate normal vectors for planes that define the dihedral angles
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a1x = vb12y*vb23z - vb12z*vb23y;
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a1y = vb12z*vb23x - vb12x*vb23z;
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a1z = vb12x*vb23y - vb12y*vb23x;
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double a1x = vb12y*vb23z - vb12z*vb23y;
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double a1y = vb12z*vb23x - vb12x*vb23z;
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double a1z = vb12x*vb23y - vb12y*vb23x;
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b1x = vb43y*vb23z - vb43z*vb23y;
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b1y = vb43z*vb23x - vb43x*vb23z;
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b1z = vb43x*vb23y - vb43y*vb23x;
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double b1x = vb43y*vb23z - vb43z*vb23y;
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double b1y = vb43z*vb23x - vb43x*vb23z;
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double b1z = vb43x*vb23y - vb43y*vb23x;
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a2x = vb23y*vb34z - vb23z*vb34y;
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a2y = vb23z*vb34x - vb23x*vb34z;
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a2z = vb23x*vb34y - vb23y*vb34x;
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double a2x = vb23y*vb34z - vb23z*vb34y;
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double a2y = vb23z*vb34x - vb23x*vb34z;
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double a2z = vb23x*vb34y - vb23y*vb34x;
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b2x = vb45y*vb43z - vb45z*vb43y;
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b2y = vb45z*vb43x - vb45x*vb43z;
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b2z = vb45x*vb43y - vb45y*vb43x;
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double b2x = vb45y*vb43z - vb45z*vb43y;
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double b2y = vb45z*vb43x - vb45x*vb43z;
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double b2z = vb45x*vb43y - vb45y*vb43x;
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// calculate terms used later in calculations
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r32 = sqrt(vb32x*vb32x + vb32y*vb32y + vb32z*vb32z);
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a1sq = a1x*a1x + a1y*a1y + a1z*a1z;
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b1sq = b1x*b1x + b1y*b1y + b1z*b1z;
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double r32 = sqrt(vb32x*vb32x + vb32y*vb32y + vb32z*vb32z);
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double a1sq = a1x*a1x + a1y*a1y + a1z*a1z;
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double b1sq = b1x*b1x + b1y*b1y + b1z*b1z;
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r43 = sqrt(vb43x*vb43x + vb43y*vb43y + vb43z*vb43z);
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a2sq = a2x*a2x + a2y*a2y + a2z*a2z;
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b2sq = b2x*b2x + b2y*b2y + b2z*b2z;
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double r43 = sqrt(vb43x*vb43x + vb43y*vb43y + vb43z*vb43z);
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double a2sq = a2x*a2x + a2y*a2y + a2z*a2z;
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double b2sq = b2x*b2x + b2y*b2y + b2z*b2z;
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if (a1sq<0.0001 || b1sq<0.0001 || a2sq<0.0001 || b2sq<0.0001) return;
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dpr21r32 = vb21x*vb32x + vb21y*vb32y + vb21z*vb32z;
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dpr34r32 = vb34x*vb32x + vb34y*vb32y + vb34z*vb32z;
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dpr32r43 = vb32x*vb43x + vb32y*vb43y + vb32z*vb43z;
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dpr45r43 = vb45x*vb43x + vb45y*vb43y + vb45z*vb43z;
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// vectors needed to calculate the cross-term dihedral angles
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double dpr21r32 = vb21x*vb32x + vb21y*vb32y + vb21z*vb32z;
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double dpr34r32 = vb34x*vb32x + vb34y*vb32y + vb34z*vb32z;
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double dpr32r43 = vb32x*vb43x + vb32y*vb43y + vb32z*vb43z;
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double dpr45r43 = vb45x*vb43x + vb45y*vb43y + vb45z*vb43z;
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// cross-term dihedral angles
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// calculate the backbone dihedral angles as VMD and GROMACS
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phi = dihedral_angle_atan2(vb21x,vb21y,vb21z,a1x,a1y,a1z,b1x,b1y,b1z,r32);
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psi = dihedral_angle_atan2(vb32x,vb32y,vb32z,a2x,a2y,a2z,b2x,b2y,b2z,r43);
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double phi = dihedral_angle_atan2(vb21x,vb21y,vb21z,a1x,a1y,a1z,b1x,b1y,b1z,r32);
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double psi = dihedral_angle_atan2(vb32x,vb32y,vb32z,a2x,a2y,a2z,b2x,b2y,b2z,r43);
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if (phi == 180.0) phi= -180.0;
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if (psi == 180.0) psi= -180.0;
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phi1 = phi;
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double phi1 = phi;
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if (phi1 < 0.0) phi1 += 360.0;
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psi1 = psi;
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double psi1 = psi;
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if (psi1 < 0.0) psi1 += 360.0;
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// find the neighbor grid point index
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li1 = int(((phi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
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li2 = int(((psi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
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li3 = int((phi-CMAPXMIN2)/CMAPDX);
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li4 = int((psi-CMAPXMIN2)/CMAPDX);
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mli3 = li3 % CMAPDIM;
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mli4 = li4 % CMAPDIM;
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mli31 = (li3+1) % CMAPDIM;
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mli41 = (li4+1) %CMAPDIM;
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mli1 = li1 % CMAPDIM;
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mli2 = li2 % CMAPDIM;
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mli11 = (li1+1) % CMAPDIM;
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mli21 = (li2+1) %CMAPDIM;
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t1 = type-1;
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int li1 = int(((phi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
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int li2 = int(((psi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
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int li3 = int((phi-CMAPXMIN2)/CMAPDX);
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int li4 = int((psi-CMAPXMIN2)/CMAPDX);
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int mli3 = li3 % CMAPDIM;
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int mli4 = li4 % CMAPDIM;
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int mli31 = (li3+1) % CMAPDIM;
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int mli41 = (li4+1) %CMAPDIM;
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int mli1 = li1 % CMAPDIM;
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int mli2 = li2 % CMAPDIM;
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int mli11 = (li1+1) % CMAPDIM;
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int mli21 = (li2+1) %CMAPDIM;
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int t1 = type-1;
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if (t1 < 0 || t1 > 5) Kokkos::abort("Invalid CMAP crossterm_type");
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// determine the values and derivatives for the grid square points
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double gs[4],d1gs[4],d2gs[4],d12gs[4];
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gs[0] = d_cmapgrid(t1,mli3,mli4);
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gs[1] = d_cmapgrid(t1,mli31,mli4);
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gs[2] = d_cmapgrid(t1,mli31,mli41);
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@ -417,84 +399,67 @@ void FixCMAPKokkos<DeviceType>::operator()(TagFixCmapPostForce, const int n, dou
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// calculate the derivatives dphi/dr_i
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dphidr1x = 1.0*r32/a1sq*a1x;
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dphidr1y = 1.0*r32/a1sq*a1y;
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dphidr1z = 1.0*r32/a1sq*a1z;
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double dphidr1x = 1.0*r32/a1sq*a1x;
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double dphidr1y = 1.0*r32/a1sq*a1y;
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double dphidr1z = 1.0*r32/a1sq*a1z;
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dphidr2x = -1.0*r32/a1sq*a1x - dpr21r32/a1sq/r32*a1x + dpr34r32/b1sq/r32*b1x;
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dphidr2y = -1.0*r32/a1sq*a1y - dpr21r32/a1sq/r32*a1y + dpr34r32/b1sq/r32*b1y;
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dphidr2z = -1.0*r32/a1sq*a1z - dpr21r32/a1sq/r32*a1z + dpr34r32/b1sq/r32*b1z;
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double dphidr2x = -1.0*r32/a1sq*a1x - dpr21r32/a1sq/r32*a1x + dpr34r32/b1sq/r32*b1x;
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double dphidr2y = -1.0*r32/a1sq*a1y - dpr21r32/a1sq/r32*a1y + dpr34r32/b1sq/r32*b1y;
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double dphidr2z = -1.0*r32/a1sq*a1z - dpr21r32/a1sq/r32*a1z + dpr34r32/b1sq/r32*b1z;
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dphidr3x = dpr34r32/b1sq/r32*b1x - dpr21r32/a1sq/r32*a1x - r32/b1sq*b1x;
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dphidr3y = dpr34r32/b1sq/r32*b1y - dpr21r32/a1sq/r32*a1y - r32/b1sq*b1y;
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dphidr3z = dpr34r32/b1sq/r32*b1z - dpr21r32/a1sq/r32*a1z - r32/b1sq*b1z;
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double dphidr3x = dpr34r32/b1sq/r32*b1x - dpr21r32/a1sq/r32*a1x - r32/b1sq*b1x;
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double dphidr3y = dpr34r32/b1sq/r32*b1y - dpr21r32/a1sq/r32*a1y - r32/b1sq*b1y;
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double dphidr3z = dpr34r32/b1sq/r32*b1z - dpr21r32/a1sq/r32*a1z - r32/b1sq*b1z;
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dphidr4x = r32/b1sq*b1x;
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dphidr4y = r32/b1sq*b1y;
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dphidr4z = r32/b1sq*b1z;
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double dphidr4x = r32/b1sq*b1x;
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double dphidr4y = r32/b1sq*b1y;
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double dphidr4z = r32/b1sq*b1z;
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// calculate the derivatives dpsi/dr_i
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dpsidr1x = 1.0*r43/a2sq*a2x;
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dpsidr1y = 1.0*r43/a2sq*a2y;
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dpsidr1z = 1.0*r43/a2sq*a2z;
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double dpsidr1x = 1.0*r43/a2sq*a2x;
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double dpsidr1y = 1.0*r43/a2sq*a2y;
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double dpsidr1z = 1.0*r43/a2sq*a2z;
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dpsidr2x = r43/a2sq*a2x + dpr32r43/a2sq/r43*a2x - dpr45r43/b2sq/r43*b2x;
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dpsidr2y = r43/a2sq*a2y + dpr32r43/a2sq/r43*a2y - dpr45r43/b2sq/r43*b2y;
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dpsidr2z = r43/a2sq*a2z + dpr32r43/a2sq/r43*a2z - dpr45r43/b2sq/r43*b2z;
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double dpsidr2x = r43/a2sq*a2x + dpr32r43/a2sq/r43*a2x - dpr45r43/b2sq/r43*b2x;
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double dpsidr2y = r43/a2sq*a2y + dpr32r43/a2sq/r43*a2y - dpr45r43/b2sq/r43*b2y;
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double dpsidr2z = r43/a2sq*a2z + dpr32r43/a2sq/r43*a2z - dpr45r43/b2sq/r43*b2z;
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dpsidr3x = dpr45r43/b2sq/r43*b2x - dpr32r43/a2sq/r43*a2x - r43/b2sq*b2x;
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dpsidr3y = dpr45r43/b2sq/r43*b2y - dpr32r43/a2sq/r43*a2y - r43/b2sq*b2y;
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dpsidr3z = dpr45r43/b2sq/r43*b2z - dpr32r43/a2sq/r43*a2z - r43/b2sq*b2z;
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double dpsidr3x = dpr45r43/b2sq/r43*b2x - dpr32r43/a2sq/r43*a2x - r43/b2sq*b2x;
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double dpsidr3y = dpr45r43/b2sq/r43*b2y - dpr32r43/a2sq/r43*a2y - r43/b2sq*b2y;
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double dpsidr3z = dpr45r43/b2sq/r43*b2z - dpr32r43/a2sq/r43*a2z - r43/b2sq*b2z;
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dpsidr4x = r43/b2sq*b2x;
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dpsidr4y = r43/b2sq*b2y;
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dpsidr4z = r43/b2sq*b2z;
|
||||
double dpsidr4x = r43/b2sq*b2x;
|
||||
double dpsidr4y = r43/b2sq*b2y;
|
||||
double dpsidr4z = r43/b2sq*b2z;
|
||||
|
||||
// calculate forces on cross-term atoms: F = -(dE/dPhi)*(dPhi/dr)
|
||||
|
||||
f1[0] = dEdPhi*dphidr1x;
|
||||
f1[1] = dEdPhi*dphidr1y;
|
||||
f1[2] = dEdPhi*dphidr1z;
|
||||
f2[0] = dEdPhi*dphidr2x + dEdPsi*dpsidr1x;
|
||||
f2[1] = dEdPhi*dphidr2y + dEdPsi*dpsidr1y;
|
||||
f2[2] = dEdPhi*dphidr2z + dEdPsi*dpsidr1z;
|
||||
f3[0] = -dEdPhi*dphidr3x - dEdPsi*dpsidr2x;
|
||||
f3[1] = -dEdPhi*dphidr3y - dEdPsi*dpsidr2y;
|
||||
f3[2] = -dEdPhi*dphidr3z - dEdPsi*dpsidr2z;
|
||||
f4[0] = -dEdPhi*dphidr4x - dEdPsi*dpsidr3x;
|
||||
f4[1] = -dEdPhi*dphidr4y - dEdPsi*dpsidr3y;
|
||||
f4[2] = -dEdPhi*dphidr4z - dEdPsi*dpsidr3z;
|
||||
f5[0] = -dEdPsi*dpsidr4x;
|
||||
f5[1] = -dEdPsi*dpsidr4y;
|
||||
f5[2] = -dEdPsi*dpsidr4z;
|
||||
|
||||
// apply force to each of the 5 atoms
|
||||
|
||||
if (i1 < nlocal) {
|
||||
d_f(i1,0) += f1[0];
|
||||
d_f(i1,1) += f1[1];
|
||||
d_f(i1,2) += f1[2];
|
||||
d_f(i1,0) += dEdPhi*dphidr1x;
|
||||
d_f(i1,1) += dEdPhi*dphidr1y;
|
||||
d_f(i1,2) += dEdPhi*dphidr1z;
|
||||
}
|
||||
if (i2 < nlocal) {
|
||||
d_f(i2,0) += f2[0];
|
||||
d_f(i2,1) += f2[1];
|
||||
d_f(i2,2) += f2[2];
|
||||
d_f(i2,0) += dEdPhi*dphidr2x + dEdPsi*dpsidr1x;
|
||||
d_f(i2,1) += dEdPhi*dphidr2y + dEdPsi*dpsidr1y;
|
||||
d_f(i2,2) += dEdPhi*dphidr2z + dEdPsi*dpsidr1z;
|
||||
}
|
||||
if (i3 < nlocal) {
|
||||
d_f(i3,0) += f3[0];
|
||||
d_f(i3,1) += f3[1];
|
||||
d_f(i3,2) += f3[2];
|
||||
d_f(i3,0) += (-dEdPhi*dphidr3x - dEdPsi*dpsidr2x);
|
||||
d_f(i3,1) += (-dEdPhi*dphidr3y - dEdPsi*dpsidr2y);
|
||||
d_f(i3,2) += (-dEdPhi*dphidr3z - dEdPsi*dpsidr2z);
|
||||
}
|
||||
if (i4 < nlocal) {
|
||||
d_f(i4,0) += f4[0];
|
||||
d_f(i4,1) += f4[1];
|
||||
d_f(i4,2) += f4[2];
|
||||
d_f(i4,0) += (-dEdPhi*dphidr4x - dEdPsi*dpsidr3x);
|
||||
d_f(i4,1) += (-dEdPhi*dphidr4y - dEdPsi*dpsidr3y);
|
||||
d_f(i4,2) += (-dEdPhi*dphidr4z - dEdPsi*dpsidr3z);
|
||||
}
|
||||
if (i5 < nlocal) {
|
||||
d_f(i5,0) += f5[0];
|
||||
d_f(i5,1) += f5[1];
|
||||
d_f(i5,2) += f5[2];
|
||||
d_f(i5,0) -= dEdPsi*dpsidr4x;
|
||||
d_f(i5,1) -= dEdPsi*dpsidr4y;
|
||||
d_f(i5,2) -= dEdPsi*dpsidr4z;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -69,6 +69,9 @@ class FixCMAPKokkos : public FixCMAP, public KokkosBase {
|
||||
ExecutionSpace space) override;
|
||||
|
||||
protected:
|
||||
|
||||
int nlocal;
|
||||
|
||||
typename AT::t_x_array d_x;
|
||||
typename AT::t_f_array d_f;
|
||||
|
||||
|
||||
Reference in New Issue
Block a user