Commit 2 JT 031219
- modified examples (gneb and spinmin now distinct) - started documention for spinmin
This commit is contained in:
julient31
@ -13,11 +13,15 @@ min_modify command :h3
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min_modify keyword values ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {dmax} or {line}
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keyword = {dmax} or {line} or {alpha_damp} or {discret_factor}
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{dmax} value = max
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max = maximum distance for line search to move (distance units)
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{line} value = {backtrack} or {quadratic} or {forcezero}
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backtrack,quadratic,forcezero = style of linesearch to use :pre
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backtrack,quadratic,forcezero = style of linesearch to use
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{alpha_damp} value = damping
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damping = fictitious Gilbert damping for spin minimization (adim)
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{discret_factor} value = factor
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factor = defines a dividing factor for adaptive spin timestep (adim) :pre
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:ule
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[Examples:]
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@ -65,6 +69,9 @@ difference of two large values (energy before and energy after) and
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that difference may be smaller than machine epsilon even if atoms
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could move in the gradient direction to reduce forces further.
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Keywords {alpha_damp} and {discret_factor} only make sense when
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a {spinmin} minimization style is declared.
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[Restrictions:] none
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[Related commands:]
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@ -11,11 +11,12 @@ min_style command :h3
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min_style style :pre
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style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul
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style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spinmin} :ul
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[Examples:]
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min_style cg
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min_style spinmin
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min_style fire :pre
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[Description:]
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@ -61,9 +62,21 @@ the velocity non-parallel to the current force vector. The velocity
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of each atom is initialized to 0.0 by this style, at the beginning of
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a minimization.
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Style {spinmin} is a damped spin dynamics with a variable
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timestep as described in "(Tranchida)"_#Tranchida.
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The value of the fictitious Gilbert damping and of the dividing
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factor for the adaptive timestep can be modified by the
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{alpha_damp} and {discret_factor} options respectively.
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Those options can be defined using the "min_modify"_min_modify.html
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command.
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Either the {quickmin} and {fire} styles are useful in the context of
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nudged elastic band (NEB) calculations via the "neb"_neb.html command.
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The {spinmin} style is useful in the context of geodesic nudged
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elastic band (GNEB) calculations via the "neb/spin"_neb_spin.html
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command.
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NOTE: The damped dynamic minimizers use whatever timestep you have
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defined via the "timestep"_timestep.html command. Often they will
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converge more quickly if you use a timestep about 10x larger than you
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@ -1,4 +1,4 @@
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# bcc iron in a 3d periodic box
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# bfo in a 3d periodic box
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units metal
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dimension 3
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@ -9,7 +9,7 @@ atom_style spin
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atom_modify map array
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lattice sc 3.96
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region box block 0.0 68.0 0.0 68.0 0.0 1.0
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region box block 0.0 34.0 0.0 34.0 0.0 1.0
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create_box 1 box
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create_atoms 1 box
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@ -17,7 +17,6 @@ create_atoms 1 box
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mass 1 1.0
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set group all spin/random 11 2.50
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#set group all spin 2.5 -1.0 0.0 0.0
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pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
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pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
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@ -30,7 +29,8 @@ neigh_modify every 10 check yes delay 20
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#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
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fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
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fix 2 all langevin/spin 0.1 0.0 21
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.1 21
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fix 3 all nve/spin lattice no
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timestep 0.0001
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@ -50,8 +50,8 @@ thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
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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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dump 200 all custom 1 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 50 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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min_style spinmin
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minimize 1.0e-6 1.0e-6 10000 10000
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#minimize 1.0e-8 1.0e-8 10000 1000
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min_modify alpha_damp 1.0 discret_factor 10.0
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minimize 0.0 0.0 10000 1000
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@ -9,7 +9,7 @@ atom_style spin
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atom_modify map array
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lattice bcc 2.8665
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region box block 0.0 4.0 0.0 4.0 0.0 1.0
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region box block 0.0 4.0 0.0 4.0 0.0 4.0
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create_box 1 box
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create_atoms 1 box
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@ -17,7 +17,7 @@ create_atoms 1 box
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mass 1 55.845
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set group all spin/random 31 2.2
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#set group all spin 2.2 -1.0 0.0 0.0
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#set group all spin 2.2 1.0 1.0 -1.0
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pair_style spin/exchange 3.5
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pair_coeff * * exchange 3.4 0.02726 0.2171 1.841
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@ -26,8 +26,9 @@ neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
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fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0
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fix 2 all langevin/spin 0.1 0.0 21
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fix 1 all precession/spin anisotropy 0.0001 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 0.1 21
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fix 3 all nve/spin lattice no
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timestep 0.0001
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@ -37,18 +38,20 @@ compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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variable magx equal c_out_mag[1]
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variable magy equal c_out_mag[2]
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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variable tmag equal c_out_mag[6]
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thermo 1
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thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
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thermo 100
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thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal
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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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dump 1 all custom 1 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 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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min_style spinmin
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minimize 1.0e-6 1.0e-6 1000 10000
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#minimize 1.0e-8 1.0e-6 1000 10000
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min_modify alpha_damp 1.0 discret_factor 10.0
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minimize 1.0e-10 1.0e-10 100000 1000
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@ -843,156 +843,12 @@ double FixNEB_spin::geodesic_distance(double spi[3], double spj[3])
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return dist;
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}
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/* ----------------------------------------------------------------------
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geometric damped advance os spins
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---------------------------------------------------------------------- */
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//void FixNEB_spin::advance_spins(double dts)
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//{
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// //int j=0;
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// //int *sametag = atom->sametag;
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// int nlocal = atom->nlocal;
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// int *mask = atom->mask;
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// double **sp = atom->sp;
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// double **fm = atom->fm;
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// double tdampx,tdampy,tdampz;
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// double msq,scale,fm2,energy,dts2;
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// double alpha;
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// double spi[3],fmi[3];
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// double cp[3],g[3];
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//
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// //cp[0] = cp[1] = cp[2] = 0.0;
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// //g[0] = g[1] = g[2] = 0.0;
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// dts2 = dts*dts;
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//
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// // fictitious Gilbert damping of 1
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// alpha = 1.0;
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//
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// // loop on all spins on proc.
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//
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// if (ireplica != nreplica-1 && ireplica != 0)
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// for (int i = 0; i < nlocal; i++)
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// if (mask[i] & groupbit) {
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//
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// spi[0] = sp[i][0];
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// spi[1] = sp[i][1];
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// spi[2] = sp[i][2];
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//
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// fmi[0] = fm[i][0];
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// fmi[1] = fm[i][1];
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// fmi[2] = fm[i][2];
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//
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// // calc. damping torque
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//
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// tdampx = -alpha*(fmi[1]*spi[2] - fmi[2]*spi[1]);
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// tdampy = -alpha*(fmi[2]*spi[0] - fmi[0]*spi[2]);
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// tdampz = -alpha*(fmi[0]*spi[1] - fmi[1]*spi[0]);
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//
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// // apply advance algorithm (geometric, norm preserving)
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//
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// fm2 = (tdampx*tdampx+tdampy*tdampy+tdampz*tdampz);
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// energy = (sp[i][0]*tdampx)+(sp[i][1]*tdampy)+(sp[i][2]*tdampz);
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//
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// cp[0] = tdampy*sp[i][2]-tdampz*sp[i][1];
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// cp[1] = tdampz*sp[i][0]-tdampx*sp[i][2];
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// cp[2] = tdampx*sp[i][1]-tdampy*sp[i][0];
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//
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// g[0] = sp[i][0]+cp[0]*dts;
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// g[1] = sp[i][1]+cp[1]*dts;
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// g[2] = sp[i][2]+cp[2]*dts;
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//
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// g[0] += (fm[i][0]*energy-0.5*sp[i][0]*fm2)*0.5*dts2;
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// g[1] += (fm[i][1]*energy-0.5*sp[i][1]*fm2)*0.5*dts2;
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// g[2] += (fm[i][2]*energy-0.5*sp[i][2]*fm2)*0.5*dts2;
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//
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// g[0] /= (1+0.25*fm2*dts2);
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// g[1] /= (1+0.25*fm2*dts2);
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// g[2] /= (1+0.25*fm2*dts2);
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//
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// sp[i][0] = g[0];
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// sp[i][1] = g[1];
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// sp[i][2] = g[2];
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//
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// // renormalization (check if necessary)
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//
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// msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
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// scale = 1.0/sqrt(msq);
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// sp[i][0] *= scale;
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// sp[i][1] *= scale;
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// sp[i][2] *= scale;
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//
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// // comm. sp[i] to atoms with same tag (for serial algo)
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//
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// // no need for simplecticity
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// //if (sector_flag == 0) {
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// // if (sametag[i] >= 0) {
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// // j = sametag[i];
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// // while (j >= 0) {
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// // sp[j][0] = sp[i][0];
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// // sp[j][1] = sp[i][1];
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// // sp[j][2] = sp[i][2];
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// // j = sametag[j];
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// // }
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// // }
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// //}
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// //
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//
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// }
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//}
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/* ----------------------------------------------------------------------
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evaluate max timestep
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---------------------------------------------------------------------- */
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//double FixNEB_spin::evaluate_dt()
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//{
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// double dtmax;
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// double fmsq;
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// double fmaxsqone,fmaxsqloc,fmaxsqall;
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// int nlocal = atom->nlocal;
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// int *mask = atom->mask;
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// double **fm = atom->fm;
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//
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// // finding max fm on this proc.
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//
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// fmsq = fmaxsqone = fmaxsqloc = fmaxsqall = 0.0;
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// for (int i = 0; i < nlocal; i++)
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// if (mask[i] & groupbit) {
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// fmsq = fm[i][0]*fm[i][0]+fm[i][1]*fm[i][1]+fm[i][2]*fm[i][2];
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// fmaxsqone = MAX(fmaxsqone,fmsq);
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// }
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//
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// // finding max fm on this replica
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//
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// fmaxsqloc = fmaxsqone;
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// MPI_Allreduce(&fmaxsqone,&fmaxsqloc,1,MPI_DOUBLE,MPI_MAX,world);
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//
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// // finding max fm over all replicas, if necessary
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// // this communicator would be invalid for multiprocess replicas
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//
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// if (update->multireplica == 1) {
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// fmaxsqall = fmaxsqloc;
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// MPI_Allreduce(&fmaxsqloc,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,universe->uworld);
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// }
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//
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// if (fmaxsqall < fmaxsqloc)
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// error->all(FLERR,"Incorrect fmaxall calc.");
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//
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// // define max timestep
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// // dividing by 10 the inverse of max frequency
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//
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// dtmax = MY_2PI/(10.0*sqrt(fmaxsqall));
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//
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// return dtmax;
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//}
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/* ----------------------------------------------------------------------
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send/recv NEB atoms to/from adjacent replicas
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received atoms matching my local atoms are stored in xprev,xnext
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replicas 0 and N-1 send but do not receive any atoms
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------------------------------------------------------------------------- */
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void FixNEB_spin::inter_replica_comm()
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{
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int i,m;
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