try snes now

brucefan1983 · Jan 19, 2025 · 4671ec2 · 4671ec2
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diff --git a/tools/for_coding/tbmd/find_cost.m b/tools/for_coding/tbmd/find_cost.m
@@ -7,8 +7,8 @@
 L=[9.483921 9.483921 9.483921];
 for n_pop = 1 : N_pop
     para=population(n_pop,:);
-    [NN,NL]=find_neighbor(N_atom,L,[1 1 1],3.6,r);
-    [f_cal]=find_force(N_atom,3,NN,NL,L,[1 1 1],r,para);
+    [NN,NL]=find_neighbor(N_atom,L,3,r);
+    [energy,f_cal]=find_force(N_atom,NN,NL,L,r,para);
     cost(n_pop) = sqrt(mean(mean((f_cal - f_ref).^2))) ...
         + 0.0e-5 * 0.5 * sum(para.^2) + 0.0e-5 * sum(abs(para));
 end
diff --git a/tools/for_coding/tbmd/find_force.m b/tools/for_coding/tbmd/find_force.m
@@ -1,6 +1,6 @@
-function [energy, force] = find_force(N, neighbor_number, neighbor_list, box, r)
+function [energy, force] = find_force(N, neighbor_number, neighbor_list, box, r, para)
     [energy_repulsive,force_repulsive]=find_force_repulsive(N, neighbor_number, neighbor_list, box, r);
-    [energy_band,force_band]=find_force_band(N, neighbor_number, neighbor_list, box, r);
+    [energy_band,force_band]=find_force_band(N, neighbor_number, neighbor_list, box, r, para);
     energy=energy_repulsive+energy_band;
     force=force_repulsive+force_band;
 end
diff --git a/tools/for_coding/tbmd/find_force_band.m b/tools/for_coding/tbmd/find_force_band.m
@@ -1,12 +1,13 @@
-function [energy, force] = find_force_band(N, neighbor_number, neighbor_list, box, r)
+function [energy, force] = find_force_band(N, neighbor_number, neighbor_list, box, r, para)
     D=3;
     N4 = N*4; N2 = N4/2; H0 = zeros(N4, N4); H  = zeros(N4, N4);
     energy = 0; force = zeros(N, D);
-    on_site_matrix = diag([-2.99, 3.71, 3.71, 3.71]);
-    v_sss = -5.0;
-    v_sps = 4.7;
-    v_pps = 5.5;
-    v_ppp = -1.55;
+    %on_site_matrix = diag([-2.99, 3.71, 3.71, 3.71]);
+    on_site_matrix = diag([para(1), para(2), para(2), para(2)]);
+    v_sss = para(3); %-5.0;
+    v_sps = para(4); %4.7;
+    v_pps = para(5); %5.5;
+    v_ppp = para(6); %-1.55;
     for n1 = 1 : N
         H(4*n1 - 3 : 4*n1, 4*n1 - 3 : 4*n1) = on_site_matrix;
         for k = 1 : neighbor_number(n1)

diff --git a/tools/for_coding/tbmd/find_force_para.m b/tools/for_coding/tbmd/find_force_para.m
diff --git a/tools/for_coding/tbmd/my_snes.m b/tools/for_coding/tbmd/my_snes.m
@@ -1,5 +1,5 @@
 function [best_fitness, elite] = my_snes(number_of_variables, maximal_generation)
-population_size = 20;
+population_size = 30;
 best_fitness = ones(maximal_generation, 1);
 elite = zeros(maximal_generation, number_of_variables);
 mu = 10*rand(1, number_of_variables)-5; % initial mean

diff --git a/tools/for_coding/tbmd/test_cohesive.m b/tools/for_coding/tbmd/test_cohesive.m
@@ -5,14 +5,16 @@
 energy_diamond=zeros(Ne,1);
 energy_graphene=zeros(Ne,1);
 
+para=[-2.99, 3.71, -5.0, 4.7, 5.5, -1.55];
+
 tic;
 for n=1:Ne
 [N_diamond,L,r]=find_diamond(2,bond_diamond(n));
 [NN,NL]=find_neighbor(N_diamond,L,3,r);
-[energy_diamond(n)]=find_force(N_diamond,NN,NL,L,r);
+[energy_diamond(n)]=find_force(N_diamond,NN,NL,L,r,para);
 [N_graphene,L,r]=find_graphene(bond_graphene(n));
 [NN,NL]=find_neighbor(N_graphene,L,3,r);
-[energy_graphene(n)]=find_force(N_graphene,NN,NL,L,r);
+[energy_graphene(n)]=find_force(N_graphene,NN,NL,L,r,para);
 end
 toc
 

diff --git a/tools/for_coding/tbmd/test_force.m b/tools/for_coding/tbmd/test_force.m
@@ -1,10 +1,12 @@
 clear; close all;
 
+para=[-2.99, 3.71, -5.0, 4.7, 5.5, -1.55];
+
 [N,L,r]=find_graphene(1.42);
 r=r+rand(N,3)*0.1;
 [NN,NL]=find_neighbor(N,L,3,r);
 tic
-[energy,f_analytical]=find_force(N,NN,NL,L,r);
+[energy,f_analytical]=find_force(N,NN,NL,L,r,para);
 toc
 
 f_finite=zeros(N,3);
@@ -14,8 +16,8 @@
     for d=1:3
     rpx=r;rpx(n,d)=rpx(n,d)+delta;
     rmx=r;rmx(n,d)=rmx(n,d)-delta;
-    [ep]=find_force(N,NN,NL,L,rpx);
-    [em]=find_force(N,NN,NL,L,rmx);
+    [ep]=find_force(N,NN,NL,L,rpx,para);
+    [em]=find_force(N,NN,NL,L,rmx,para);
     f_finite(n,d)=(em-ep)/(2*delta);
     end
     toc

diff --git a/tools/for_coding/tbmd/test_size_effects.m b/tools/for_coding/tbmd/test_size_effects.m
@@ -3,11 +3,13 @@
 energy_diamond=zeros(Ne,1);
 N_diamond=zeros(Ne,1);
 
+para=[-2.99, 3.71, -5.0, 4.7, 5.5, -1.55];
+
 tic;
 for n=1:Ne
 [N_diamond(n),L,r]=find_diamond(n,1.55);
 [NN,NL]=find_neighbor(N_diamond(n),L,3,r);
-[energy_diamond(n)]=find_force(N_diamond(n),NN,NL,L,r);
+[energy_diamond(n)]=find_force(N_diamond(n),NN,NL,L,r,para);
 end
 toc
 

diff --git a/tools/for_coding/tbmd/test_snes.m b/tools/for_coding/tbmd/test_snes.m
@@ -1,8 +1,8 @@
 clear; close all;
 
 % Call my_snes to evolve
-dim = 7;
-[best_fitness, elite] = my_snes(dim, 1000);
+dim = 6;
+[best_fitness, elite] = my_snes(dim, 100);
 num_generations = length(best_fitness);
 
 % Evolution of the best fitness: