Mechanical properties calculation for a system of particles bounded in chains.
Perform a calculation of the characteristic properties of lipid chains in bilayer membrane (diffusivity, pressure profile, radial density plot...).
Required:OpenGl, optional CGAL.

Command list:

All the commands that can be typed in the command line can be written in the argument list with a single dash "-" for single characters or with double dash "--" for words.

"d" Graphics(argc,argv); "?" Legenda(); "!" printf("Insert a shell command: "); "dens" DensProf(NBin,NSample,Coord); "3to2" From3To2d(NSample,Param[0]); "3to1" From3To1d(Coord); "2to1" From2To1d(Coord); "pro" ProjectionF(NBin,Coord); "core" CoreF(NSample,0); "coreNano" CoreF(NSample,1); "RadShell" RadialShell(NBin); "angle" Angle(NBin); "SlabProf" SlabProf(NBin,nNano,CoordProfile); "SlabAngleProfs" SlabAngleProfs(NBin,10,CoordProfile); "CartDens" CartDens(NBin,nNano); "radNano" RadDistrF(NBin,1,nNano); "radCm" RadDistrF(NBin,0,nNano); "radCmN" RadDistrF(NBin,2,nNano); "radStalk" RadDistrF(NBin,4,nNano); "radPore" RadDistrF(NBin,5,nNano); "cartNano" RadDistrF(NBin,6,nNano); "BondDistr" BondDistr(NSample); "SplayDistr" SplayDistr(NSample); "cm" CenterOfMass(Coord); "Dens2Thick" RadDens2Thick(NBin); "Dens2Thick2d" RadDens2Thick2d(NBin); "ThickFromDens" ThickFromDens(NBin); "temp" Temperature(NBin,Coord); "nano" NanoParticle(NBin); "surf" Surface(NBin,1); "diff" Diffusivity(); "DiffSlab" DiffSlab(NSample); "PairCorr" PairCorr(NBin,1); "pairMon" PairCorrelationF(NBin,0); "pairChain" PairCorrelationF(NBin,1); "pairRound" PairCorrelationF(NBin,2); "pairSquare" PairCorrelationF(NBin,3); "pairPep" PairCorrelationF(NBin,4); "AvSnap" AvSnap(); "scatt" ScatteringF(NBin,0); "scatt2" ScatteringF(NBin,1); "worm" WormF(20,NBin); "header" HeaderAverage(nNano); "spe" SpectrumF(NSample); "RadNormPos" RadNormPos(NBin,NSample); "AreaDistr" AreaDistrF(NBin); "mid" Midplane(NSample); "midSpe" SpectrumMidplane(NSample); "prop" PropertiesF(); "divOpp" DivideLayers(VAR_OPPOSED); "divTube" DivideLayers(VAR_TUBE); "divVes" DivideLayers(VAR_VESICLE); "AreaCompr" AreaCompr(NSample); "PTrace" PressTrace(); "PRadial" PressRadial(); "Tens" SurfTens(NBin); "TensCartRad" Tens2dCartRad(); "SumTens" SumTens(); "Prova" Prova(); "stalk" StalkF(32); "StalkLine" StalkLineProfF(NBin); "BackBone" BackBone(Line,NBin); "rem" RemoveChains(); "ChPos" FILE *FWrite = fopen("ChainPos.dat","w"); for(int c=0;c<pNChain();c++){ fprintf(FWrite,"%lf %lf %lf\n",Ch[c].Pos[0],Ch[c].Pos[1],Ch[c].Pos[2]); } fclose(FWrite); "tra" Transform(nBlock); Write("transformed.dat"); "xyz" WriteXyz("resume.dat"); "ConvLattice" ConvLattice(NSample,"LatticePoints.dat"); "write" Write("resume.dat"); "WidomOut" WidomOut("NrgLipid.dat",NBin); WidomOut(); "WidomIn" WidomIn("NrgLipid.dat",NBin); WidomIn(); "End2End" End2EndDistr("End2EndDistr"); "ElCoup" ElasticCoupling(NSample); "ElCoupNVT" ElasticCouplingNVT(); "E2EDec" Decoupling(1); "SmoothGrid" SmoothGrid(NBin,"GridSmoothed.dat"); "IsoSurf" IsoSurf(NSample,Param,NParam); "IsoLine" NParam = 10; double OldParam = Param[0]; for(int p=0;p<NParam;p++){ Param[p] = OldParam*p/(double)(NParam); } IsoLine(NSample,Param,NParam,0); "IsoLineDens" IsoLine(NSample,Param,NParam,1); "FPore" FetchPore(); "FStalk" FetchStalk(); "AStalk" StalkArea(); "Shift2Center" Shift2Center(); "AvSnap" AvSnap(); "DirDec" Decoupling(0); "BilDist" BilayerDistance("BilayerDistance.dat",NSample); "Bond" BondDistr("BondDistr.dat",NBin); "Diff2Dens" Diff2Files(NSample,1); "Diff2Pre" Diff2Files(NSample,0); "RestPre" RestPress(NBin); "tecplotDens" Conv2Tecplot(NBin,0); "tecplotPre" Conv2Tecplot(NBin,1); "tecplotHei" Conv2Tecplot(NBin,2); "rzd" Conv2rzd(NBin); "xyzd" Conv2xyzd(NBin); "vmd" Conv2Vmd(); "povray" Conv2Povray(); "coord" printf("Enter coordinate number [0 2] or radius [3]: "); scanf("%d",&Coord); if(Coord < 0 || Coord > 3){ printf("Value not valid, coord set to 0\n"); Coord = 0; } "norm" printf("Enter the direction of the normal: "); int Temp = 0; scanf("%d",&Temp); if(Temp >= 0 && Temp < 3){ CNorm = Temp; CLat1 = (CNorm+1)%3; CLat2 = (CNorm+2)%3; printf("n %d c1 %d c2 %d\n",CNorm,CLat1,CLat2); } "type" int NChType = CHAIN_EVERY; printf("up %d down %d flabby %d stretch %d added %d every %d: ",CHAIN_UP,CHAIN_DOWN,CHAIN_FLABBY,CHAIN_STRETCH,CHAIN_ADDED,CHAIN_EVERY); scanf("%d",&NChType); if(NChType != CHAIN_UP && NChType != CHAIN_DOWN && NChType != CHAIN_FLABBY && NChType != CHAIN_STRETCH && NChType != CHAIN_ADDED && NChType != CHAIN_EVERY){ printf("Value not valid, type set to %d\n",CHAIN_EVERY); NChType = CHAIN_EVERY; } NChType = NChType; "file" ChangeFile(); "val" printf("Number bins (NBin) :"); scanf("%d",&NBin); "Nei" FindNeighbours("CrossLinks.dat"); "sample" Sample(NSample); "open" char InFile[256]; printf("New file name: "); scanf("%s",Comando); sprintf(InFile,Comando); OpenFile(InFile); ">" quando++; if(quando >= NFile){ quando = 0; } if(quando >=0 && quando < NFile){ OpenFile(quando); printf("Opening: %s\n",argv[FilePos[quando]]); } "<" quando–; if(quando < 0){ quando = NFile-1; } if(quando >=0 && quando < NFile){ OpenFile(quando); printf("Opening: %s\n",argv[FilePos[quando]]); } "f" printf("Open file num 0-%d: ",NFile); scanf("%d",&quando); if( quando >= 0 && quando < NFile){ OpenFile(quando); } "info" printf("------------------------------------------------------\n"); char cSystem[STRSIZE]; SysInfo(cSystem); printf("%s\n",cSystem); SysDef(cSystem); printf("%s\n",cSystem);

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