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Commit JT 040319
- improved examples - start rework gneb init. (Rodrigues' formula)
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julient31
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@ -1,5 +1,10 @@
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Perform geodesic NEB calculations for spin configurations.
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The two examples are:
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- the magnetic switching of an iron nanoisland
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- the collapse of a magnetic skyrmion
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Run those examples as:
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mpirun -np 4 lmp_mpi -in in.gneb.iron -partition 4x1
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mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1
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You should be able to use any number of replicas >= 3.
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@ -1,4 +1,3 @@
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# bcc iron in a 3d periodic box
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units metal
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dimension 3
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@ -11,6 +10,7 @@ atom_modify map array
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read_data initial.iron_spin
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# setting mass, mag. moments, and interactions for bcc iron
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# (mass not necessary for fixed lattice calculation)
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mass 1 55.845
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@ -1,4 +1,3 @@
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# bcc iron in a 3d periodic box
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units metal
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dimension 3
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@ -8,17 +7,12 @@ atom_style spin
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# necessary for the serial algorithm (sametag)
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atom_modify map array
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#lattice sc 3.0
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#region box block 0.0 20.0 0.0 20.0 0.0 1.0
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#create_box 1 box
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#create_atoms 1 box
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read_data initial.skyrmion
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# setting mass, mag. moments, and interactions for bcc iron
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# (mass not necessary for fixed lattice calculation)
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mass 1 55.845
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#set group all spin 2.2 -1.0 0.0 0.0
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pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
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pair_coeff * * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211
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@ -31,10 +25,8 @@ fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.0 21
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fix 3 all neb/spin 1.0
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#fix 4 all nve/spin lattice no
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timestep 0.0001
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#run 0
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compute out_mag all spin
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variable magx equal c_out_mag[1]
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@ -49,10 +41,8 @@ thermo_modify format float %20.15g
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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variable u universe 1 2 3 4
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#dump 1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
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dump 1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
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min_style spin
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min_modify alpha_damp 1.0 discret_factor 10.0
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neb/spin 1.0e-16 1.0e-16 1000 1000 10 final final.skyrmion
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#neb/spin 1.0e-16 1.0e-16 10 10 10 final final.skyrmion
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min_modify alpha_damp 1.0 discrete_factor 10.0
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neb/spin 1.0e-12 1.0e-12 10000 10000 10 final final.skyrmion
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@ -637,52 +637,9 @@ void NEB_spin::initial_rotation(double *spi, double *sploc, double fraction)
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// initial, final and inter ang. values
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double itheta,iphi,ftheta,fphi,ktheta,kphi;
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double spix,spiy,spiz,spfx,spfy,spfz;
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double spkx,spky,spkz,iknorm;
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spix = spi[0];
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spiy = spi[1];
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spiz = spi[2];
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spfx = sploc[0];
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spfy = sploc[1];
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spfz = sploc[2];
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iphi = itheta = fphi = ftheta = 0.0;
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iphi = acos(spiz);
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if (sin(iphi) != 0.0)
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itheta = acos(spix/sin(iphi));
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fphi = acos(spfz);
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if (sin(fphi) != 0.0)
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ftheta = acos(spfx/sin(fphi));
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kphi = iphi + fraction*(fphi-iphi);
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ktheta = itheta + fraction*(ftheta-itheta);
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spkx = cos(ktheta)*sin(kphi);
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spky = sin(ktheta)*sin(kphi);
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spkz = cos(kphi);
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double knormsq = spkx*spkx + spky*spky + spkz*spkz;
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if (knormsq != 0.0)
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iknorm = 1.0/sqrt(knormsq);
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spkx *= iknorm;
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spky *= iknorm;
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spkz *= iknorm;
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//sploc[0] = spkx;
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//sploc[1] = spky;
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//sploc[2] = spkz;
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//double kx,ky,kz;
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//double itheta,iphi,ftheta,fphi,ktheta,kphi;
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//double spix,spiy,spiz,spfx,spfy,spfz;
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//double kcrossx,kcrossy,kcrossz,knormsq;
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//double spkx,spky,spkz;
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//double sdot,omega,iknorm;
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//double spkx,spky,spkz,iknorm;
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//spix = spi[0];
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//spiy = spi[1];
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@ -691,40 +648,89 @@ void NEB_spin::initial_rotation(double *spi, double *sploc, double fraction)
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//spfx = sploc[0];
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//spfy = sploc[1];
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//spfz = sploc[2];
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//
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//kx = spiy*spfz - spiz*spfy;
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//ky = spiz*spfx - spix*spfz;
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//kz = spix*spfy - spiy*spfx;
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//knormsq = kx*kx+ky*ky+kz*kz;
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//
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//if (knormsq != 0.0) {
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//iphi = itheta = fphi = ftheta = 0.0;
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//iphi = acos(spiz);
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//if (sin(iphi) != 0.0)
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// itheta = acos(spix/sin(iphi));
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//fphi = acos(spfz);
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//if (sin(fphi) != 0.0)
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// ftheta = acos(spfx/sin(fphi));
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//kphi = iphi + fraction*(fphi-iphi);
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//ktheta = itheta + fraction*(ftheta-itheta);
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//spkx = cos(ktheta)*sin(kphi);
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//spky = sin(ktheta)*sin(kphi);
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//spkz = cos(kphi);
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//double knormsq = spkx*spkx + spky*spky + spkz*spkz;
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//if (knormsq != 0.0)
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// iknorm = 1.0/sqrt(knormsq);
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// kx *= iknorm;
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// ky *= iknorm;
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// kz *= iknorm;
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//}
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//
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//kcrossx = ky*spiz - kz*spiy;
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//kcrossy = kz*spix - kx*spiz;
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//kcrossz = kx*spiy - ky*spix;
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//sdot = spix*spfx + spiy*spfy + spiz*spfz;
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//omega = acos(sdot);
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//omega *= fraction;
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//spkx = spix*cos(omega) + kcrossx*sin(omega);
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//spky = spiy*cos(omega) + kcrossy*sin(omega);
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//spkz = spiz*cos(omega) + kcrossz*sin(omega);
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//
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//iknorm = 1.0/sqrt(spkx*spkx+spky*spky+spkz*spkz);
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//if (iknorm == 0.0)
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// error->all(FLERR,"Incorrect rotation operation");
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//spkx *= iknorm;
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//spky *= iknorm;
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//spkz *= iknorm;
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//sploc[0] = spkx;
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//sploc[1] = spky;
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//sploc[2] = spkz;
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double kx,ky,kz;
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double spix,spiy,spiz,spfx,spfy,spfz;
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double kcrossx,kcrossy,kcrossz,knormsq;
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double kdots;
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double spkx,spky,spkz;
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double sdot,omega,iknorm,isnorm;
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spix = spi[0];
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spiy = spi[1];
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spiz = spi[2];
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spfx = sploc[0];
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spfy = sploc[1];
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spfz = sploc[2];
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kx = spiy*spfz - spiz*spfy;
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ky = spiz*spfx - spix*spfz;
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kz = spix*spfy - spiy*spfx;
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knormsq = kx*kx+ky*ky+kz*kz;
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if (knormsq != 0.0) {
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iknorm = 1.0/sqrt(knormsq);
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kx *= iknorm;
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ky *= iknorm;
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kz *= iknorm;
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}
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kcrossx = ky*spiz - kz*spiy;
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kcrossy = kz*spix - kx*spiz;
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kcrossz = kx*spiy - ky*spix;
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kdots = kx*spix + ky*spiz + kz*spiz;
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sdot = spix*spfx + spiy*spfy + spiz*spfz;
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omega = acos(sdot);
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omega *= fraction;
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spkx = spix*cos(omega) + kcrossx*sin(omega);
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spky = spiy*cos(omega) + kcrossy*sin(omega);
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spkz = spiz*cos(omega) + kcrossz*sin(omega);
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spkx += kx*kdots*(1.0-cos(omega));
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spky += ky*kdots*(1.0-cos(omega));
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spkz += kz*kdots*(1.0-cos(omega));
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isnorm = 1.0/sqrt(spkx*spkx+spky*spky+spkz*spkz);
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if (isnorm == 0.0)
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error->all(FLERR,"Incorrect rotation operation");
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spkx *= isnorm;
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spky *= isnorm;
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spkz *= isnorm;
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sploc[0] = spkx;
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sploc[1] = spky;
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