_Normal_input_darwin_v12.m

%makeinput_v11_auto_copyall_SBATCH_remesh_input_mass_ratio
%clc
clear all
close all
fclose all;

%cd ('C:\running_tasks\')
%folderlist=dir('*r83');

copyall_or_not=0;
%account='SOGA';% zl352
account='LIANG-SL3';%dl359 xz328 fy hj

ristart=587;%407;
ri=ristart-1;
s=0;
for gi=[0.4]
    for ai=[
0.075
]'
        for mi=[
1.50
                ]'
            ri=ri+1;
            temp1=['g',num2str(gi,'%.1f'),'a',num2str(ai,'%.3f'), ...
                'm',num2str(mi,'%.1f'),'r',num2str(ri)];
            mkdir(temp1)
            disp(temp1)

            
            s=s+1;
            txt{s}=['cd ./*r',num2str(ri),'; chmod u+x suball.com; ./suball.com; cd ../'];

        end
    end
end


%% write submit.com file
fid = fopen(['./',num2str(ristart),'_to_',num2str(ri),'_subauto_hpc'], 'w');              
for ii = 1:length(txt)
        fprintf(fid,'%s\n', txt{ii});
end


%%
start_task_num=ristart;
end_task_num=ri;%117+18-1;

nn=end_task_num-start_task_num+1;
for ii=1:nn
    task_num=start_task_num+ii-1;
    folderlist=dir(['*r',num2str(task_num)]);
    foldername=folderlist.name;
    disp(foldername)
    

    walltime='12:00:00'; %Wall clock time
    codename='7';


    
    %Global Calculation parameters
    ttperiods=120;
    odfis=1000;% Output data frequency in steps
    misfve=12000;% Maximum iteration step for velocity equation
    misfppe=10000;% Maximum iteration step for Pressure Possion equation
    NITRB= '350';       % MAXIMUM ITERATION STEP FOR MESH UPDATE EUQATION 
    AERB = '1.D-15';      % ALLOW ERROR FOR SOLVING THE MESH UPDATE EQUATION
    % NITRB= '350'; By convention
    % AERB = '1.D-15'; By convention
    %mkdir (foldername)
    cd (foldername)
    mkdir('00')
    rmdir('0*','s');
    str=foldername;
    str(str=='r')=[' '];
    str(str=='u')=[];
    str(str=='n')=[];
    str(str=='_')=[];
    str(str=='z')=[];
    str(str=='l')=[' '];
    str1=str;
    str(str=='g')=' ';
    str(str=='a')=' ';
    str(str=='m')=' ';
    gam=str2num(str);


    %% INPUT PARAMETERs 1
    g=gam(1);%G/D
    a1=gam(2);%A1
    m=gam(3);%m*
    re=100;  %Renolds Number
    ftspara=0.00025;%normally 0.00025 for interaction of two cylinders
    
    

    

    taskstr=['r',num2str(gam(4))]        ;%task number
    %% Adjust Title Format
    gstr=num2str(g,'%.2f');%    ,'%.3f'
    a1str=num2str(a1,'%.3f');%  ,'%.3f'
    mstr=num2str(m);%,'%.1f'
    
    protodir=['/Users/zhonglulin/Documents/OneDrive - University Of Cambridge/OneDrive/PhDWorks/VIV/Chosen_mesh_19_Dec/g',num2str(g,'%.1f')];
    
    
    %% =============================FOLDERs====================== f1s to be run

    %---
    i=0;
    j=0;
    s=0;
    clear txt
    for j=[0.81:0.01:0.99]
        if j==0.85||j==0.90||j==0.95
            continue
        end
        name=['0',num2str(j,'%05.3f'),''];
        mkdir(name) 
        %end
        s=s+1;
        txt{s}=['cd ./',name,'; qsub slurm_submit.txt; cd ../'];
    end
    %% write suball.com file
    fid = fopen(['./suball.com'], 'w');              
    for ii = 1:length(txt)
            fprintf(fid,'%s\n', txt{ii});
    end
    disp('folder created')
    %%



    %% =============================COPY1======================

    if copyall_or_not

    disp('copying from proto...')
    
    origindir=pwd;
    
    cd (protodir)
    list1=dir('*.TXT');
    n1=length(list1);

    cd (origindir)
    list0=dir('0*');
    n0=length(list0);

    %%
    %n0=3;%for test
    %%
    for j=1:n0
        for i=1:n1
            origin=[protodir,'/',list1(i).name];
            destin=['./',list0(j).name];
            copyfile(origin,destin)
        end
    end
    disp('copy done')



    %% =============================COPY2======================



    %%
    %n0=3;%for test
    %%
%     for j=1:n0
%         for i=1:n1
%             origin=['./proto/',list1(i).name];
%             destin=['./',list0(j).name];
%             copyfile(origin,destin)
%         end
%     end
%     disp('copy done')

    %% ===========================
    end % end of copy

    %% =============================EDIT======================
    %clear all
    %close all

    list0=dir('0*');
    n0=length(list0);

    %n0=3;%test f=0.05



    %%
    disp(['alter value for ','G/D=',gstr,', A1=',a1str,', m*=',mstr])

    for j=1:n0
        %% Calculated INPUT PARAMETERs
        %disp(['alter value for ','G/D=',num2str(g),', A1=',num2str(a1),', m*=',num2str(m), ...,
        %    ' f1=',list0(j).name])
        f1=str2num(list0(j).name);
        visc=2*3.14159265*f1*a1/re; %viscosity
        fts=ftspara/(2*3.14159265*a1*f1); %flow time step
    
        tts=ttperiods/f1/fts;% total time step

        
        f1str=list0(j).name;
        taskname=['Z',f1str,taskstr];
        %taskdirdarwin=['cd /home/zl352/VIVHPC/','g',gstr,'a',a1str,'m',mstr,'zl_',taskstr,'_code',codename,'/',list0(j).name];
        %taskdirorange=['cd /projects/y73/dongfang/','g',gstr,'a',a1str,'m',mstr,'zl_',taskstr,'_code',codename,'/',list0(j).name];
        %taskdirdarwin=['cd ~/scratch/','g',gstr,'a',a1str,'m',mstr,'zl_',taskstr,'/',list0(j).name];
        taskdirdarwin='cd $workdir';
        taskdirorange=['cd /projects/y73/dongfang/','g',gstr,'a',a1str,'m',mstr,'zl_',taskstr,'/',list0(j).name];
    %%   Reading and edit txt
        %
        origindir=pwd;
        cd (protodir)
        fid = fopen('VIV_PARA.TXT','r');
        i = 1;
        tline = fgetl(fid);
        txtv{i} = tline;
        while ischar(tline)
            i = i+1;
            tline = fgetl(fid);
            txtv{i} = tline;
        end
        fclose(fid);

        % Change cell 
        txtv{3} = [strrep(sprintf('%d',a1),'e','D'),'    -> amplitude of the forced vibration'];
        txtv{4} = [strrep(sprintf('%d',f1),'e','D'),'    -> frequency (1/period) of the forced vibration'];
        txtv{9} = [mstr,'   -> mass ratio'];
        % 
    %% 
        fid = fopen('CALCULATION_PARA.TXT','r');
        i = 1;
        tline = fgetl(fid);
        txtc{i} = tline;
        while ischar(tline)
            i = i+1;
            tline = fgetl(fid);
            txtc{i} = tline;
        end
        fclose(fid);

        % Change cell
        txtc{1} = [strrep(sprintf('%d',visc),'e','D'),'       --> viscosity'];
        txtc{2} = [strrep(sprintf('%d',fts),'e','D'),'       --> FLOW TIME STEP'];
        txtc{4} = [num2str(tts),'         --> Total time steps'];
        txtc{5} = [num2str(odfis),'         --> Output data frequency in steps'];
        txtc{7} = [num2str(misfve),'         --> Maximum iteration step for velocity equation'];
        txtc{10} = [num2str(misfppe),'         --> Maximum iteration step for Pressure Possion equation'];
        txtc{14} = [NITRB,'         --> MAXIMUM ITERATION STEP FOR MESH UPDATE EUQATION '];
        txtc{15} = [AERB,'         --> ALLOW ERROR FOR SOLVING THE MESH UPDATE EQUATION'];

        %% SLURM
        fid = fopen('slurm_submit.txt','r');
        i = 1;
        tline = fgetl(fid);
        txts{i} = tline;
        while ischar(tline)
            i = i+1;
            tline = fgetl(fid);
            txts{i} = tline;
        end
        fclose(fid);

        % Change cell

        txts{13} = ['#SBATCH -J ',taskname];
        txts{15} = ['#SBATCH -A ',account];
        txts{21} = ['#!SBATCH --mem=200'];
        txts{24} = ['#SBATCH --time=',walltime];
        txts{25} = ['#SBATCH --mail-user=zl352'];
        txts{26} = ['#SBATCH --mail-type=END'];
        %txts{63} = ['application="/home/zl352/VIVHPC/code',codename,'/viv"']; %code dir
        txts{63} = ['application="~/scratch/code',codename,'/viv"']; %code dir
        txts{107} = taskdirdarwin;     %running dir 
        %txts{107} = 'cd $workdir';

       %% PBS
        fid = fopen('pbs.sh','r');
        i = 1;
        tline = fgetl(fid);
        txtp{i} = tline;
        while ischar(tline)
            i = i+1;
            tline = fgetl(fid);
            txtp{i} = tline;
        end
        fclose(fid);

        % Change cell
        txtp{3} = ['#PBS -l walltime=',walltime];
        txtp{6} = ['#PBS -N ',taskname];
        txtp{7} = taskdirorange;
        txtp{8} = ['/projects/y73/dongfang/code',codename,'/viv > test.e'];
    %%  write txt
        cd (origindir)
        cd (list0(j).name)
        fid = fopen('VIV_PARA.TXT', 'w');
        for i = 1:numel(txtv)
            if txtv{i+1} == -1
                fprintf(fid,'%s', txtv{i});
                break
            else
                fprintf(fid,'%s\n', txtv{i});
            end
        end

        fid = fopen('CALCULATION_PARA.TXT', 'w');
        for i = 1:numel(txtc)
            if txtc{i+1} == -1
                fprintf(fid,'%s', txtc{i});
                break
            else
                fprintf(fid,'%s\n', txtc{i});
            end
        end

        fid = fopen('slurm_submit.txt', 'w');
        for i = 1:numel(txts)
            if txts{i+1} == -1
                fprintf(fid,'%s', txts{i});
                break
            else
                fprintf(fid,'%s\n', txts{i});
            end
        end

        fid = fopen('pbs.sh', 'w');
        for i = 1:numel(txtp)
            if txtp{i+1} == -1
                fprintf(fid,'%s', txtp{i});
                break
            else
                fprintf(fid,'%s\n', txtp{i});
            end
        end
    %%
       fclose(fid);
       cd ('../')
    end
    disp(['NOTE! codename= ',codename])
    disp(['NOTE! flow_time_step_para= ',num2str(ftspara)])
    disp(['NOTE! taskdir_darwin= ',taskdirdarwin])
    disp(['NOTE! taskdir_orange= ',taskdirorange])
    disp(['NOTE! walltime= ', walltime])
    disp('====================================')
    
    fclose all;
    cd ('../')
end