diff --git a/examples/SPIN/gneb/README b/examples/SPIN/gneb/README index eeb4aa4692..7d388d898e 100644 --- a/examples/SPIN/gneb/README +++ b/examples/SPIN/gneb/README @@ -1,5 +1,5 @@ -Run this example as: +Run those examples as: -mpirun -np 3 lmp_g++ -partition 3x1 -in in.tad +mpirun -np 4 lmp_mpi -in in.gneb.iron -partition 4x1 You should be able to use any number of replicas >= 3. diff --git a/examples/SPIN/gneb/interpolate/README b/examples/SPIN/gneb/interpolate/README new file mode 100644 index 0000000000..d0f75226c5 --- /dev/null +++ b/examples/SPIN/gneb/interpolate/README @@ -0,0 +1,7 @@ +Interpolate.x tries to perform a cubic polynomial interpolation +of the MEP found + +Compile the program with: +gcc interpolate.c -o interpolate.x -lm -lgsl + + diff --git a/examples/SPIN/gneb/interpolate/interpolate.c b/examples/SPIN/gneb/interpolate/interpolate.c new file mode 100644 index 0000000000..48804d53a2 --- /dev/null +++ b/examples/SPIN/gneb/interpolate/interpolate.c @@ -0,0 +1,109 @@ +/* ------------------------------------------------------------------------ + Provide some explanation here +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + This program is a courtesy of Aleksei Ivanov (Univ. of Iceland) + Contributing authors: Aleksei Ivanov (Univ. of Iceland), + Julien Tranchida (SNL) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include + +// calculate cubic coefficients + +void count_coefficient(double *V, double *F, double *R, double *a, double *b, + double *c,double *d,int M){ + /* R = square of distance between images*/ + /* V = energy of images */ + /* F = projection of real real forces along the path? */ + int i; + for(i = 0; i < M ; i++) { + a[i] = ( -2.0*(V[i+1]-V[i])/R[i] - F[i] - F[i+1] ) / (R[i]*R[i]); + //a[i] = ( -2.0*(V[i+1]-V[i])/sqrt(R[i]) - F[i] - F[i+1] ) / R[i]; + b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*R[i] ) / (R[i]*R[i]); + //b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*sqrt(R[i]) ) / R[i]; + c[i] = -F[i]; + d[i] = V[i]; + } +} + +// cubic spline + +double spline(double a,double b,double c,double d,double x) { + return (a*x*x*x + b*x*x + c*x + d); +} + +int main() { + int M=0; // M+1 = number of images + double *fmdottan; // projection of real forces on tangent path + double *coords; // initial value of reaction coords + double *V; // energy of images + double *dist; // square of the distance between images + double *a, *b, *c, *d ; // coefficients of cubic functions + double x; // reaction coordinate + double A,B; // additional variables for rnd + double length = 0.0; + int i,j; + FILE *data; + + printf("Enter M = number of images - 1 \n"); + scanf("%d",&M); + + // allocating and initializing tables + + a = calloc(M,sizeof(double)); // cubic coefficients + b = calloc(M,sizeof(double)); + c = calloc(M,sizeof(double)); + d = calloc(M,sizeof(double)); + V = calloc((M+1),sizeof(double)); // energies + coords = calloc((M+1),sizeof(double)); // reaction coordinates + fmdottan = calloc((M+1),sizeof(double)); // fm dot tangent + dist = calloc(M+1,sizeof(double)); // distance between images + + // reading input file + + if((data=fopen("reac_coords_iron_verbose.dat","r")) == NULL) { + //if((data=fopen("neb_init.dat","r")) == NULL) { + printf("Incorrect input file name."); + return 0; + } + + for(j=0; j < M+1; j++) { + fscanf(data,"%lf\t%lf\t%lf\t%lf\n",&coords[j],&V[j],&fmdottan[j],&dist[j]); + length += dist[j]; + printf("%lf %lf %lf %lf\n",coords[j],V[j],fmdottan[j],dist[j]); + } + + if( (fclose(data)) == 0) { + printf("Data stored, input file closed.\n "); + } + + // calculate value of coefficients + + count_coefficient(V,fmdottan,dist,a,b,c,d,M); + + // plot result of the interpolation + + if( ( data=fopen("interpolation_result.dat","w") )== NULL) { + printf("Interpolation file could not be open."); + return 0; + } + + A = B = 0.0; + for(i = 0; i < M ; i++) { + B += dist[i]; + printf("%13le\n",B); + for(j = 0; j <= 1000; j++) { + x = dist[i]*1.0e-3*j; + fprintf(data,"%13lf\t%13le\n",(x+A)/length,spline(a[i],b[i],c[i],d[i],x)); + } + A += dist[i]; + } + + return 0; +} diff --git a/examples/SPIN/gneb/interpolate/reac_coords_iron_verbose.dat b/examples/SPIN/gneb/interpolate/reac_coords_iron_verbose.dat new file mode 100644 index 0000000000..7a56274a31 --- /dev/null +++ b/examples/SPIN/gneb/interpolate/reac_coords_iron_verbose.dat @@ -0,0 +1,8 @@ +0.0000000 -3.915271 3.4995081e-17 2.4573077 +0.14285714 -3.9148148 -0.00059075739 2.4573077 +0.28571429 -3.9136926 -0.00072315767 2.4573077 +0.42857143 -3.9127883 -0.0003191228 2.4573265 +0.57142857 -3.9127883 0.0003191228 2.4403341 +0.71428571 -3.9136926 0.00072315767 2.4044093 +0.85714286 -3.9148148 0.00059075739 2.3766041 +1.0000000 -3.915271 -4.1231828e-17 0.0000000 diff --git a/examples/SPIN/gneb/final.iron_spin b/examples/SPIN/gneb/iron/final.iron_spin similarity index 100% rename from examples/SPIN/gneb/final.iron_spin rename to examples/SPIN/gneb/iron/final.iron_spin diff --git a/examples/SPIN/gneb/in.gneb.iron b/examples/SPIN/gneb/iron/in.gneb.iron similarity index 70% rename from examples/SPIN/gneb/in.gneb.iron rename to examples/SPIN/gneb/iron/in.gneb.iron index a8028392a1..4cfbd723b7 100644 --- a/examples/SPIN/gneb/in.gneb.iron +++ b/examples/SPIN/gneb/iron/in.gneb.iron @@ -8,17 +8,11 @@ atom_style spin # necessary for the serial algorithm (sametag) atom_modify map array -lattice bcc 2.8665 -region box block 0.0 4.0 0.0 4.0 0.0 1.0 -#create_box 1 box -#create_atoms 1 box - read_data initial.iron_spin # setting mass, mag. moments, and interactions for bcc iron mass 1 55.845 -#set group all spin 2.2 -1.0 0.0 0.0 pair_style spin/exchange 3.5 pair_coeff * * exchange 3.4 0.02726 0.2171 1.841 @@ -28,9 +22,7 @@ neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.0001 1.0 0.0 0.0 fix_modify 1 energy yes -fix 2 all langevin/spin 0.0 0.0 21 fix 3 all neb/spin 1.0 -#fix 4 all nve/spin lattice no timestep 0.0001 thermo 100 @@ -52,10 +44,8 @@ thermo_modify format float %20.15g compute outsp all property/atom spx spy spz sp fmx fmy fmz variable u universe 1 2 3 4 -#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] dump 1 all custom 200 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3] min_style spin -min_modify alpha_damp 1.0 discret_factor 10.0 -neb/spin 1.0e-12 1.0e-12 50000 50000 10 final final.iron_spin -#neb/spin 1.0e-6 1.0e-6 1000 10 10 final final.iron_spin +min_modify alpha_damp 1.0 discrete_factor 10.0 +neb/spin 1.0e-12 1.0e-12 200000 100000 1000 final final.iron_spin verbose diff --git a/examples/SPIN/gneb/initial.iron_spin b/examples/SPIN/gneb/iron/initial.iron_spin similarity index 100% rename from examples/SPIN/gneb/initial.iron_spin rename 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57.0 0.0 0.0 0.0 1.0 diff --git a/examples/SPIN/gneb/skyrmion/in.gneb.skyrmion b/examples/SPIN/gneb/skyrmion/in.gneb.skyrmion new file mode 100644 index 0000000000..aab6376e98 --- /dev/null +++ b/examples/SPIN/gneb/skyrmion/in.gneb.skyrmion @@ -0,0 +1,58 @@ +# bcc iron in a 3d periodic box + +units metal +dimension 3 +boundary p p f +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array + +#lattice sc 3.0 +#region box block 0.0 20.0 0.0 20.0 0.0 1.0 +#create_box 1 box +#create_atoms 1 box + +read_data initial.skyrmion + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +#set group all spin 2.2 -1.0 0.0 0.0 + +pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1 +pair_coeff * * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211 +pair_coeff * * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 +fix_modify 1 energy yes +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all neb/spin 1.0 +#fix 4 all nve/spin lattice no + +timestep 0.0001 +#run 0 + +compute out_mag all spin +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] + +thermo 100 +thermo_style custom step time v_magx v_magz v_magnorm etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +variable u universe 1 2 3 4 +#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] +dump 1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +min_style spin +min_modify alpha_damp 1.0 discret_factor 10.0 +neb/spin 1.0e-16 1.0e-16 1000 1000 10 final final.skyrmion +#neb/spin 1.0e-16 1.0e-16 10 10 10 final final.skyrmion diff --git a/examples/SPIN/gneb/skyrmion/initial.skyrmion b/examples/SPIN/gneb/skyrmion/initial.skyrmion new file mode 100644 index 0000000000..f940aee182 --- /dev/null +++ b/examples/SPIN/gneb/skyrmion/initial.skyrmion @@ -0,0 +1,818 @@ +LAMMPS data file via write_data, version 28 Feb 2019, timestep = 6 + +400 atoms +1 atom types + +0.0000000000000000e+00 6.0000000000000000e+01 xlo xhi +0.0000000000000000e+00 6.0000000000000000e+01 ylo yhi +0.0000000000000000e+00 3.0000000000000000e+00 zlo zhi + +Masses + +1 55.845 + +Atoms # spin + +1 1 2.5000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -3.9693242391277868e-03 -3.9693242391277929e-03 9.9998424434096433e-01 0 0 0 +21 1 2.5000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.1868011343002482e-02 -4.8145058779812530e-03 9.9991798205648519e-01 0 0 0 +41 1 2.5000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.9561861499557517e-02 -6.5828744882500201e-03 9.9978697697966845e-01 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5dcd27ef2b..d981962a70 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -283,7 +283,7 @@ void NEB_spin::run() fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan ... GradVNdottan\n"); + "GradV0dottan DN0 ... GradVNdottan DNN\n"); } else { fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " @@ -296,7 +296,7 @@ void NEB_spin::run() fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan ... GradVNdottan\n"); + "GradV0dottan DN0 ... GradVNdottan DNN\n"); } else { fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " @@ -368,7 +368,7 @@ void NEB_spin::run() fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan ... GradVNdottan\n"); + "GradV0dottan DN0... GradVNdottan DNN\n"); } else { fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc " @@ -381,7 +381,7 @@ void NEB_spin::run() fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN " - "GradV0dottan ... GradVNdottan\n"); + "GradV0dottan DN0 ... GradVNdottan DNN\n"); } else { fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque " "GradV0 GradV1 GradVc " @@ -873,8 +873,9 @@ void NEB_spin::print_status() for (int i = 0; i < nreplica; i++) fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]); if (verbose) { - for (int i = 0; i < nreplica; i++) - fprintf(uscreen,"%12.8g ",all[i][5]); + for (int i = 0; i < nreplica-1; i++) + fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]); + fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); } fprintf(uscreen,"\n"); } @@ -888,8 +889,9 @@ void NEB_spin::print_status() for (int i = 0; i < nreplica; i++) fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]); if (verbose) { - for (int i = 0; i < nreplica; i++) - fprintf(ulogfile,"%12.8g ",all[i][5]); + for (int i = 0; i < nreplica-1; i++) + fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]); + fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]); } fprintf(ulogfile,"\n"); fflush(ulogfile);