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free_cylinder_input_darwin_v15_Re_varies.m
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free_cylinder_input_darwin_v15_Re_varies.m
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%% To use the same config as "Flow mediated interactions between two cylinders at finite Re numbers"
%% in order to validate the numerical method.
%makeinput_v11_auto_copyall_SBATCH_remesh_input_mass_ratio
%this version can deal with damping 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');
% damp f
% Gtarget=0.4;
% A1target=0.025;
% mtarget=1.5;
% damptarget=[
% 0.00
% 0.05
% 0.10
% 0.20
% 0.40
% ];
% f1target=[ % corresponding each damp
% 0.78
% 0.78
% 0.78
% 0.795
% 0.9
% ];
copyall_or_not=1;
ttperiods=500;
account='SOGA'; % zl352
codename='8'; %to remove the spring (restoring force)
%account='LIANG-SL3';%dl359 xz328 fy hj
ristart=2056;%;
ri=ristart-1;
s=0;
%%{
if1=[
1
]';
%}
%if1=[0.379 0.757];
%if1=[2.8:0.4:10];
% if1=[
% 0.35
% 0.36
% 0.37
% 0.38
% 0.39
% 0.4
% 0.41
% 0.42
% 0.43
% 0.44
% 0.45
%
% 0.705
% 0.71
% 0.715
% 0.72
% 0.725
% 0.73
% 0.735
% 0.74
% 0.745
% 00.750
% 0.755
% 0.76
% 0.765
% 0.77
% 0.775
% 0.78
% 0.785
% 0.79
% 0.795
% ]';
%re=100;% Reynolds Number
for sn=1:1
if sn==1
ristart2=ristart;
else
ristart2=ri+1;
end
if sn==1 %A1 varies
gii=[
0.4
0.5
0.6
0.7
0.8
0.9
1.0
1.5
2.0
2.5
3.0
]';% s=1.5, d=2.5
aii=gii/2;
mii=[1:0.5:2];
dampii=[0];
reii=[5:10:200];
end
disp(['total number of cases =',num2str(length(gii)*length(aii)*length(mii)*length(dampii)*length(reii))])
pause
clear txt
for gi=gii
for ai=aii
for mi=mii
for dampi=dampii
for rei=reii
ri=ri+1;
temp1=['g',num2str(gi,'%.1f'),...
'a',num2str(ai,'%.3f'), ...
'm',num2str(mi,'%.1f'),...
'd',num2str(dampi,'%.2f'),...
'e',num2str(rei,'%.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
end
end
disp('===1st level folders created===')
%% write submit.com file
fid = fopen(['./',num2str(ristart2),'_to_',num2str(ri),'_subauto_hpc'], 'w');
for ii = 1:length(txt)
fprintf(fid,'%s\n', txt{ii});
end
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
%Global Calculation parameters
odfis=2000;% 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')=' ';
str(str=='d')=' ';
str(str=='e')=' ';
gam=str2num(str);
%% INPUT PARAMETERs 1
g=gam(1);%G/D
a1=gam(2);%A1
m=gam(3);%m*
damp=gam(4);%damp ratio
re=gam(5); %Renolds Number
ftspara=0.00025;%normally 0.00025 for interaction of two cylinders
taskstr=['r',num2str(gam(end))] ;%task number
%% Adjust Title Format
gstr=num2str(g,'%.2f');% ,'%.3f'
a1str=num2str(a1,'%.3f');% ,'%.3f'
mstr=num2str(m);%,'%.1f'
dampstr=num2str(damp,'%.2f');
restr=num2str(re,'%.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,' damp=',dampstr,' re=',restr])
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=['f',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=['Not in use: 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'];
txtv{11} = [dampstr,' -> damping factor of cylinder 2'];
%
%%
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('====================================')
fclose all;
cd ('../')
end