input_darwin_v12_b1_for_1period_anime.m

%makeinput_v11_auto_copyall_SBATCH_remesh_input_mass_ratio
%clc
clear all
close all
fclose all;
cd('/Users/zhonglulin/Documents/OneDrive - University Of Cambridge/OneDrive/PhDWorks/VIV')
%cd ('C:\running_tasks\')
%folderlist=dir('*r83');



copyall_or_not=1;
ttperiods=1;%maximum periods in each run
odfis=2;% Output data frequency in steps

%account='SOGA';% zl352

account='LIANG-SL3';%dl359 xz328 fy hj

ristart=1169;%;
ri=ristart-1;
s=0;
%{
if1=[
00.050
00.100
00.150
00.200
00.250
00.300
00.350
00.375
00.400
00.425
00.450
00.500
00.550
00.600
00.650
00.700
00.750
00.800
00.825
00.850
00.900
00.950
01.000
01.100
01.200
01.300
01.400
01.600
01.800
02.000
02.400]';
%}
%if1=[0.379 0.757];

if1=[
2.5
3
3.5
4
4.5
5
5.5
6
6.5
7
7.5
8
8.5
9
9.5
10
10.5
11
11.5
12
]';

re=100;% Reynolds Number

for gi=[0.4]
    for ai=[
%0.005 0.025 0.05 0.075 0.1
0.075
]
        for mi=[
%1.50 1.7 2.0 2.2 2.5
1.5
                ]
            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
    
    %odfis=1;% 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*
      %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
    %% j=if1
    for j=if1
    %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=floor(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('====================================')
    disp(pwd)
    disp(['NOTE! acount: ',account])
    disp(['NOTE! Output step ',num2str(odfis)])
    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(['NOTE! Reynolds number= ', num2str(re)])
    disp('====================================')
    
    fclose all;
    cd ('../')
end