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runDNS.m
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runDNS.m
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%% Intro
% This is the main file for the DNS
% It will call all the other routines
function [flowHandles, info] = runDNS(caseFile, extraParameters) %#ok<*STOUT>
%% Define case file
if nargin == 0
caseFile = 'parameters';
end
%% Define if simulation will actually be compiled and run or if just the preprocessing will be done
runSimulation = true;
compileCode = true;
plotDNSDomain = false;
%% Compiling parameters
forceRecompileAll = false;
displayCompiling = false;
optimizeCode = true;
debugger = false;
profiler = false;
%% Set folders for libraries
matlabDir = ''; % Leave empty for automatic directory
decompDir = '/usr/local/2decomp_fft';
%% Data logging
logAll = false; % Save all iterations to log or just when a flow is saved
%% Run parameters file
eval(caseFile);
if nargin == 2
extraVars = unpackStruct(extraParameters);
for i = 1:length(extraVars)
eval([extraVars{i} ' = extraParameters.' extraVars{i} ';'])
end
end
%% Check if 2D or 3D
tridimensional = mesh.z.n + mesh.z.buffer.i.n + mesh.z.buffer.f.n > 1; %#ok<*NODEF>
if ~tridimensional
p_col = 1;
end
%% Add source code path
addpath source
addpath source/boundaries
%% Initialize log file
if ~exist(caseName,'dir')
mkdir(caseName);
end
fprintf('Parameters file: %s\nCase name: %s\n', caseFile, caseName);
if ~exist([caseName '/log.txt'],'file')
logFile = fopen([caseName '/log.txt'],'w');
fprintf(logFile,'Save number\tIteration\tSimulation time\tdt \tCFL \tU change\tV change\tW change\tR change\tE change');
if isfield(mesh,'trackedPoints')
for i = 1:size(mesh.trackedPoints,1)
fprintf(logFile,'\tU%d \tV%d \tW%d \tR%d \tE%d ',i,i,i,i,i);
end
end
fprintf(logFile,'\n');
fclose(logFile);
end
%% Run preprocessing routine or reload previous
if ~exist([caseName '/bin'],'dir')
mkdir([caseName '/bin'])
end
if forceRecompileAll
compileCode = true;
delete([caseName '/bin/*.mod']);
delete([caseName '/bin/*.o']);
end
fprintf('Running preprocessor\n')
preprocessing
fprintf('Mesh size: %d x %d x %d\n', mesh.nx, mesh.ny, mesh.nz)
%% Generate initial flow if needed
if genInitialFlow % If there is no previous run, generate new initial flow
fprintf('Generating new initial flow\n');
%Compute initial flow
flow = generateInitialFlow(mesh,flowParameters,flowType.initial,boundary.insideWall,flowType.name);
% Save initial flow to file
flowToSave = flow;
flowToSave.t = 0;
for var = 'UVWRE'
flowToSave.(var)(boundary.insideWall) = nan;
end
save([caseName '/flow_0000000000.mat'],'-struct','flowToSave','-v7.3');
if isfield(flowType.initial,'meanFile')
flowTypeTemp.initial.type = 'file';
flowTypeTemp.initial.flowFile = flowType.initial.meanFile;
if isfield(flowType.initial,'meshFile')
flowTypeTemp.initial.meshFile = flowType.initial.meshFile;
end
meanFlow = generateInitialFlow(mesh,flowParameters,flowTypeTemp.initial,boundary.insideWall,flowType.name);
% Save initial flow to file
flowToSave = meanFlow;
flowToSave.t = 0;
for var = 'UVWRE'
flowToSave.(var)(boundary.insideWall) = nan;
end
save([caseName '/meanflowSFD.mat'],'-struct','flowToSave','-v7.3');
end
else
fprintf('Resuming from file number %d\n',time.nStep)
end
% Copy parameters file to Fortran folder and write to log2.txt
logFile2 = fopen([caseName '/bin/log2.txt'],'a');
fprintf(logFile2,'DNS started at %s\n', datestr(now,'dd-mmm-yyyy HH:MM:SS'));
fprintf(logFile2,'Parameters file: %s\n', [caseFile '.m']);
fprintf(logFile2,'Starting flow file: flow_%.10d.mat\n\n', time.nStep);
if exist([caseName '/bin/parameters.m'],'file')
[parametersDiffStatus,parametersDiff] = system(['diff ' caseName '/bin/parameters.m ' caseFile '.m']);
if parametersDiffStatus
fprintf(logFile2,'Parameters file was changed:\n%s\n', parametersDiff);
end
end
fclose(logFile2);
copyfile([caseFile '.m'],[caseName '/bin/parameters.m']);
if nargin == 2
save([caseName '/bin/extraParameters.mat'], '-struct', 'extraParameters')
end
% Compile code
if compileCode
fprintf('Compiling code\n')
compileFortran
end
%% Plot domain
if plotDNSDomain
plotDomain %#ok<*UNRCH>
drawnow
end
%% Call Fortran code
if runSimulation && ~debugger && ~profiler
fprintf('Starting code\n')
tic
system(['cd ' caseName '/bin && mpirun -np ' num2str(p_row*p_col) ' main ' caseName]);
toc
elseif runSimulation && debugger
fprintf('Starting code with debugger\n')
system(['cd ' caseName '/bin && mpirun -n ' num2str(p_row*p_col) ' xterm -sl 1000000 -fg white -bg black -hold -e gdb -ex run --args ./main ' caseName]);
elseif runSimulation && profiler
fprintf('Starting code with profiler\n')
system('export GMON_OUT_PREFIX=''gmon.out''');
tic
system(['cd ' caseName '/bin && mpirun -np ' num2str(p_row*p_col) ' main ' caseName]);
toc
system(['cd ' caseName '/bin && gprof -l main gmon.out > profile.txt']);
system(['mv ' caseName '/bin/profile.txt .']);
end
%% Write to log2 file
logFile2 = fopen([caseName '/bin/log2.txt'],'a');
fprintf(logFile2,'DNS finished at %s\n\n', datestr(now,'dd-mmm-yyyy HH:MM:SS'));
fclose(logFile2);
%% Get outputs if needed
if nargout > 0
allCaseFiles = dir(caseName);
flowHandles = {};
for i = 1:length(allCaseFiles)
name = allCaseFiles(i).name;
if length(name) == 19 && ~isempty(regexp(name,'flow_\d*.mat','once'))
flowHandles{end+1} = matfile([caseName '/' name]); %#ok<AGROW>
end
end
end
if nargout == 2
allVars = whos;
for i = 1:length(allVars)
eval(['info.' allVars(i).name ' = ' allVars(i).name ';']);
end
end
end
function varList = unpackStruct(structure)
varList = {};
varNames = fieldnames(structure);
for i = 1:length(varNames)
varName = varNames{i};
if isstruct(structure.(varName))
varList2 = unpackStruct(structure.(varName));
for j = 1:length(varList2)
varList{end+1} = [varName '.' varList2{j}];
end
else
varList{end+1} = varName;
end
end
end