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Copy pathRe_KC_sync_input_darwin_v14_Re_varies.m
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Re_KC_sync_input_darwin_v14_Re_varies.m
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%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
%account='LIANG-SL4';%dl359 xz328 fy hj
ristart=1590;%;
ri=ristart-1;
s=0;
%%{
if1=[
% 00.050
% 00.150
% 00.200
% 00.250
% 00.300
% 0.35
% 0.36
% 0.37
% 0.38
% 0.39
% 0.4
% 0.41
% 0.42
% 0.43
% 0.44
% 0.45
% 00.500
% 00.550
% 00.600
% 00.650
% 00.700
% 0.71
% 0.72
% 0.73
% 0.74
% 0.75
% 0.76
% 0.77
% 0.78
% 0.79
% 0.795
% 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
00.050
00.100
00.150
00.200
00.250
00.300
00.350
00.360
00.370
00.380
00.390
00.400
00.410
00.420
00.430
00.440
00.450
00.500
00.550
00.600
00.650
00.700
00.705
00.710
00.715
00.720
00.725
00.730
00.735
00.740
00.745
00.750
00.755
00.760
00.765
00.770
00.775
00.780
00.785
00.790
00.795
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=[2.8:0.4:10];
% 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=[3];
aii=[
0.1592
0.3183
0.4775
0.6366
0.7958
0.9549
1.1141
1.2732
1.4324
1.5915
1.7507
1.9099
];
mii=[2];
dampii=[0.00,0.02];
reii=[
35.0000
70.0000
105.0000
140.0000
175.0000
210.0000
245.0000
280.0000
315.0000
350.0000
385.0000
420.0000]';
end
if sn==2 %m* varies
gii=0.9;
aii=0.4775;
mii=[1.5, 1.7, 2.0, 2.2, 2.5];
dampii=[0,0.05, 0.1,0.2];
reii=[50,70];
end
if sn==3 %G varies
gii=0.9;
aii=0.4775;
mii=[1.5, 1.7, 2.0, 2.2, 2.5];
dampii=[0,0.05, 0.1,0.2];
reii=[90,110];
end
clear txt
for gi=gii
for mi=mii
for dampi=dampii
for iar=1:length(aii)
if length(aii)~=length(reii)
stop%
end
%for ai=aii
%for rei=reii
ai=aii(iar);
rei=reii(iar);
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
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
codename='7';
%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,'%.3f');
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