HW1 Auxiliary Scripts

Auxiliary Scripts

write_lmp.m

%This function writes the file equivalent to meafile(dynamo) in LAMMPS
function write_lmpmeam(filename1,filename2,parameter)

fid = fopen(filename1,'wt');

fprintf(fid,'  #MEAM data\n'); 
fprintf(fid,'  # elt       lat     z       ielement     atwt\n');
fprintf(fid,'  # alpha     b0      b1      b2           b3       alat    esub    asub\n');
fprintf(fid,'  # t0        t1              t2           t3               rozero  ibar\n\n');

fprintf(fid,'''%s'' ''%s'' %u %u %f \n',parameter.elt, parameter.lat, ...
            parameter.z, parameter.ielement, parameter.atwt);
fprintf(fid,'%f %f %f %f %f %f %f %f \n',parameter.alpha, parameter.b0, ...
            parameter.b1, parameter.b2, parameter.b3, parameter.alat, ...
            parameter.esub, parameter.asub);
fprintf(fid,'%d %f %f %f %d %d \n', parameter.t0, parameter.t1, parameter.t2, ...
            parameter.t3, parameter.rozero, parameter.ibar);
        
fclose(fid);

fid = fopen(filename2, 'wt');

fprintf(fid,'augt1=0\nialloy=1\nnn2(1,1)=1\n');
fprintf(fid,'rc=%f \n', parameter.rcut);
fprintf(fid,'rho0(1)=%f\n',parameter.rozero);

fclose(fid);

find_energy.m

function [var] = find_energy(outfile, str)

var = 0;
fid = fopen(outfile);

tline = fgetl(fid);
while ~feof(fid)
   matches = strfind(tline, str);
   num = length(matches);
   if num > 0
       C = textscan(tline, '%*s %f %f');
       var = C{1}; 
       %fprintf(1,'%s \n',tline);
   end
   tline = fgetl(fid);
end

fclose(fid);

objfun1.m

function f = objfun1(x)

beta = []; model = []; w = []; goal = [];
load('objfunw.mat')

f = 0;
for i = 1:length(w)
    if w(i) ~= 0
        load(['objfun' num2str(i) '.mat'])
        D = x2fx(x,model);
        f = f + w(i)*(beta'*D'-goal(i))^2;
    end
end
end

Remove_Output_Files

rm c11_fit.log c12_fit.log c44_fit.log c11_fit.gif c12_fit.gif c44_fit.gif c11_fit.gp c12_fit.gp
rm c44_fit.gp Al.meam Al.meam.init alpha_para.txt c11_report.lammps c12_report.lammps
rm c44_report.lammps datafile dump.E0 dump.gsfe.E dump.gsfe.I dump.oct dump.surf100 dump.surf110
rm dump.surf111 dump.tet dump.vac gnuplot.report infile_relax library.meam library.meam.init log.E0
rm log.gsfe.E log.gsfe.I log.lammps log.oct log.surf100 log.surf110 log.surf111 log.tet log.vac
rm report.lammps responses.txt summary Al_coarse_pot_eval_data.mat parameter.mat Al_LHS_v1.mat
rm Al_Uncertainty_Ecoh.mat Al_weights.mat *_para.txt goal.mat objfun*.mat objfunw.mat
rm t*_para.txt log Progress_Script dump