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ns_simDynamics.m
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function ns_simDynamics(bs,delta,psi,mu,taut,nvf,...
nstf,taun,taua,mun,nrst,asp,runTm,tmSt,svPt,edpc,rpc)
% clearvars;
% [bs,delta,psi,mu,taut,nvf,nstf,taun,taua,mun,nrst,asp,runTm,tmSt,svPt,edpc,rpc]=...
% deal(6,10,1,1.25,10,0.8,50,1,1,0,1,0.25,40,0.01,10,0.15,1);
%% Specify parameters for initical configurations
% Here, we categorize these parameterse into two categories, geometric
% parameters and mechanical parameters. Denote a set of geometric
% parameters as 'gm_p' and a set of mechanical parameters as 'mc_p'. If
% we want to add paramters, just add more elements in each variable.
[gmp,mcp]=deal(struct);
[gmp.tgAr,gmp.sstn,gmp.bs,gmp.edpc,gmp.asp]=deal(1,0,bs,edpc,asp);
[mcp.del,mcp.psi,mcp.mu,mcp.taut,mcp.nvf,mcp.nstf,mcp.taun,...
mcp.taua,mcp.mun,mcp.nrst]=...
deal(delta,psi,mu,taut,nvf,nstf,taun,taua,mun,nrst);
[gmp.nFa,gmp.lsc,gmp.dt]=...
deal(gmp.bs^2,mcp.psi*sqrt(gmp.tgAr),tmSt);
[gmp.major,gmp.minor]=deal(sqrt(mcp.nvf*mcp.psi/pi/gmp.asp),...
sqrt(mcp.nvf*mcp.psi/pi*gmp.asp));
[gmp.runTm,gmp.svPt]=deal(runTm,svPt);
gmp.shEd=0.01*2*sqrt(pi);
gmp.ellDis=[gmp.major*(cos(0:pi/30:2*pi-pi/30)).',...
gmp.minor*(sin(0:pi/30:2*pi-pi/30)).';gmp.major,0];
gmp.ellAng=[mod(atan2(gmp.ellDis(1:end-1,2),gmp.ellDis(1:end-1,1)),2*pi);2*pi];
gmp.ellDis=sqrt(sum(gmp.ellDis.^2,2));
%% Generate initial configuration
[vrtx,edge,face,rg]=ns_initialConf(gmp.bs);
%% Relaxation of the configuration with extracellular spaces.
[itc,ttMx,ttTm]=deal(0,10*mcp.taut,0);
gmp.eLnc=ns_edgeLenAll(edge,gmp);
while (ttTm<=ttMx)
[vrtx,edge,face]=ns_iteration(vrtx,edge,face,rg,gmp,mcp);
itc=itc+1;
ttTm=ttTm+gmp.dt;
if mod(itc,5)==0
eLn=ns_edgeLenAll(edge,gmp);
t1Id=find(eLn<gmp.shEd);
if isempty(t1Id)==0
for jj=1:size(t1Id,1)
chk=min(face{1}(edge{1}(t1Id(jj),rg.ei(2):rg.ef(2)),rg.fi(5)));
if chk>3 && gmp.eLnc(t1Id(jj))>eLn(t1Id(jj))
[vrtx,edge,face]=...
ns_t1Transition(vrtx,edge,face,rg,gmp,mcp,t1Id(jj));
end
end
end
gmp.eLnc=ns_edgeLenAll(edge,gmp);
end
%% Compute t4t1 transition
for ii=1:size(vrtx,1)
[vrtx,edge,face]=...
ns_t4AdjacentTransition(vrtx,edge,face,rg,gmp,mcp,ii);
end
end
%
%% Relaxation of the configuration with extracellular spaces.
[itc,ttMx,ttTm,exc]=deal(0,runTm*mcp.taut,0,1);
ttDtPt=ttMx/gmp.dt/svPt;
dtPt=4000;
dtc=1;
[vr,ed1,ed2,ed3,ed4,fa1,fa2,fa3]=deal(cell(min(dtPt,ttDtPt),1));
odir=sprintf('dyn/nvf%s_nstf%s_mu%s_mun%s_taun%s_taut%s_nrst%s_asp%s/',num2str(nvf),...
num2str(nstf),num2str(mu),num2str(mun),num2str(taun),num2str(taut),num2str(nrst),num2str(asp));
odir=strrep(odir,'.','d');
if ~exist(odir,'dir')
mkdir(odir);
end
while (ttTm<=ttMx)
[vrtx,edge,face]=ns_iteration(vrtx,edge,face,rg,gmp,mcp);
itc=itc+1;
ttTm=ttTm+gmp.dt;
if mod(itc,5)==0
eLn=ns_edgeLenAll(edge,gmp);
t1Id=find(eLn<gmp.shEd);
if isempty(t1Id)==0
for jj=1:size(t1Id,1)
chk=min(face{1}(edge{1}(t1Id(jj),rg.ei(2):rg.ef(2)),rg.fi(5)));
if chk>3 && gmp.eLnc(t1Id(jj))>eLn(t1Id(jj))
[vrtx,edge,face]=...
ns_t1Transition(vrtx,edge,face,rg,gmp,mcp,t1Id(jj));
end
end
end
gmp.eLnc=ns_edgeLenAll(edge,gmp);
end
if mod(itc,5)==2
%% Compute t4t1 transition
for ii=1:size(vrtx,1)
[vrtx,edge,face]=...
ns_t4AdjacentTransition(vrtx,edge,face,rg,gmp,mcp,ii);
end
end
if mod(itc,svPt)==3
[vr{exc},ed1{exc},ed2{exc},ed3{exc},ed4{exc},fa1{exc},...
fa2{exc},fa3{exc}]=deal(vrtx,edge{1},edge{2},edge{3},...
edge{4},face{1},face{2},face{3});
exc=exc+1;
if exc==dtPt+1
save(sprintf('%s/vr_r%d_d%d.mat',odir,rpc,dtc),'vr');
save(sprintf('%s/ed1_r%d_d%d.mat',odir,rpc,dtc),'ed1');
save(sprintf('%s/ed2_r%d_d%d.mat',odir,rpc,dtc),'ed2');
save(sprintf('%s/ed3_r%d_d%d.mat',odir,rpc,dtc),'ed3');
save(sprintf('%s/ed4_r%d_d%d.mat',odir,rpc,dtc),'ed4');
save(sprintf('%s/fa1_r%d_d%d.mat',odir,rpc,dtc),'fa1');
save(sprintf('%s/fa2_r%d_d%d.mat',odir,rpc,dtc),'fa2');
save(sprintf('%s/fa3_r%d_d%d.mat',odir,rpc,dtc),'fa3');
dtc=dtc+1;
exc=1;
ttDtPt=ttDtPt-dtPt;
[vr,ed1,ed2,ed3,ed4,fa1,fa2,fa3]=...
deal(cell(min(dtPt,ttDtPt),1));
end
end
end
if exc>1
vr=vr(1:exc-1);
ed1=ed1(1:exc-1);
ed2=ed2(1:exc-1);
ed3=ed3(1:exc-1);
ed4=ed4(1:exc-1);
fa1=fa1(1:exc-1);
fa2=fa2(1:exc-1);
fa3=fa3(1:exc-1);
save(sprintf('%s/vr_r%d_d%d.mat',odir,rpc,dtc),'vr');
save(sprintf('%s/ed1_r%d_d%d.mat',odir,rpc,dtc),'ed1');
save(sprintf('%s/ed2_r%d_d%d.mat',odir,rpc,dtc),'ed2');
save(sprintf('%s/ed3_r%d_d%d.mat',odir,rpc,dtc),'ed3');
save(sprintf('%s/ed4_r%d_d%d.mat',odir,rpc,dtc),'ed4');
save(sprintf('%s/fa1_r%d_d%d.mat',odir,rpc,dtc),'fa1');
save(sprintf('%s/fa2_r%d_d%d.mat',odir,rpc,dtc),'fa2');
save(sprintf('%s/fa3_r%d_d%d.mat',odir,rpc,dtc),'fa3');
end
ns_exportParameter(gmp,mcp,odir,rpc);
%
end