int main() {
InputMap mcp( "gcmol.json" );
Tspace spc( mcp );
spc.load( "state", Tspace::RESIZE );
auto pot = Energy::Nonbonded<Tspace,Tpairpot>(mcp);
Move::Propagator<Tspace> mv( mcp, pot, spc );
EnergyDrift sys;
sys.init( Energy::systemEnergy( spc,pot,spc.p ) );
cout << atom.info() << pot.info() << textio::header( "MC Simulation Begins!" );
MCLoop loop( mcp );
while ( loop[0] ) {
while ( loop[1] )
sys += mv.move();
cout << loop.timing();
}
sys.checkDrift( Energy::systemEnergy( spc,pot,spc.p ) );
spc.save("state");
FormatPQR::save("confout.pqr", spc.p, spc.geo.len);
UnitTest test( mcp );
sys.test( test );
mv.test( test );
cout << loop.info() << sys.info() << spc.info() << mv.info() << test.info() << endl;
return test.numFailed();
}
int main() {
::atom.includefile("stockmayer.json"); // load atom properties
InputMap in("stockmayer.input"); // open parameter file for user input
Energy::NonbondedVector<Tspace,Tpair> pot(in); // non-bonded only
EnergyDrift sys; // class for tracking system energy drifts
Tspace spc(in); // create simulation space, particles etc.
Group sol;
sol.addParticles(spc, in); // group for particles
MCLoop loop(in); // class for mc loop counting
Analysis::RadialDistribution<> rdf(0.05); // particle-particle g(r)
Analysis::Table2D<double,Average<double> > mucorr(0.1); // particle-particle g(r)
TmoveTran trans(in,pot,spc);
TmoveRot rot(in,pot,spc);
trans.setGroup(sol); // tells move class to act on sol group
rot.setGroup(sol); // tells move class to act on sol group
spc.load("state");
spc.p = spc.trial;
UnitTest test(in); // class for unit testing
FormatXTC xtc(spc.geo.len.norm());
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // initial energy
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
if (slp_global() > 0.5)
sys+=trans.move( sol.size() ); // translate
else
sys+=rot.move( sol.size() ); // rotate
if (slp_global()<1.5)
for (auto i=sol.front(); i<sol.back(); i++) { // salt rdf
for (auto j=i+1; j<=sol.back(); j++) {
double r =spc.geo.dist(spc.p[i],spc.p[j]);
rdf(r)++;
mucorr(r) += spc.p[i].mu.dot(spc.p[j].mu);
}
}
if (slp_global()>0.99)
xtc.save(textio::prefix+"out.xtc", spc.p);
}
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing();
}
// perform unit tests
trans.test(test);
rot.test(test);
sys.test(test);
FormatPQR().save("confout.pqr", spc.p);
rdf.save("gofr.dat"); // save g(r) to disk
mucorr.save("mucorr.dat"); // save g(r) to disk
std::cout << spc.info() + pot.info() + trans.info()
+ rot.info() + sys.info() + test.info(); // final info
spc.save("state");
return test.numFailed();
}
int main() {
InputMap mcp("grand.input"); // open user input file
Tspace spc(mcp); // simulation space
Energy::Nonbonded<Tspace,CoulombHS> pot(mcp); // hamiltonian
pot.setSpace(spc); // share space w. hamiltonian
Group salt; // group for salt particles
salt.addParticles(spc, mcp);
spc.load("state",Tspace::RESIZE); // load old config. from disk (if any)
// Two different Widom analysis methods
double lB = Coulomb(mcp).bjerrumLength(); // get bjerrum length
Analysis::Widom<PointParticle> widom1; // widom analysis (I)
Analysis::WidomScaled<Tspace> widom2(lB,1); // ...and (II)
widom1.add(spc.p);
widom2.add(spc.p);
Move::GrandCanonicalSalt<Tspace> gc(mcp,pot,spc,salt);
Move::AtomicTranslation<Tspace> mv(mcp,pot,spc);
mv.setGroup(salt);
EnergyDrift sys; // class for tracking system energy drifts
sys.init(Energy::systemEnergy(spc,pot,spc.p));// store initial total system energy
cout << atom.info() + spc.info() + pot.info() + "\n";
MCLoop loop(mcp); // class for handling mc loops
while ( loop[0] ) {
while ( loop[1] ) {
if (slp_global() < 0.5)
sys+=mv.move( salt.size() ); // translate salt
else
sys+=gc.move(); // grand canonical exchange
widom1.sample(spc,pot,1);
widom2.sample(spc.p,spc.geo);
} // end of micro loop
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // calc. energy drift
cout << loop.timing();
} // end of macro loop
FormatPQR::save("confout.pqr", spc.p); // PQR snapshot for VMD etc.
spc.save("state"); // final simulation state
UnitTest test(mcp); // class for unit testing
gc.test(test);
mv.test(test);
sys.test(test);
widom1.test(test);
cout << loop.info() + sys.info() + mv.info() + gc.info() + test.info()
+ widom1.info() + widom2.info();
return test.numFailed();
}
int main() {
//::atom.includefile("stockmayer.json"); // load atom properties
InputMap in("stockmayer.input"); // open parameter file for user input
Energy::NonbondedVector<Tspace,Tpair> pot(in); // non-bonded only
EnergyDrift sys; // class for tracking system energy drifts
Tspace spc(in); // create simulation space, particles etc.
Group sol;
sol.addParticles(spc, in); // group for particles
MCLoop loop(in); // class for mc loop counting
TmoveTran trans(in,pot,spc);
TmoveRot rot(in,pot,spc);
trans.setGroup(sol); // tells move class to act on sol group
rot.setGroup(sol); // tells move class to act on sol group
spc.load("state");
spc.trial = spc.p;
UnitTest test(in); // class for unit testing
Analysis::DipoleAnalysis dian(spc,in);
DipoleWRL sdp;
FormatXTC xtc(spc.geo.len.norm());
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // initial energy
while ( loop[0] ) { // Markov chain
while ( loop[1] ) {
if (slp_global() > 0.5)
sys+=trans.move( sol.size() ); // translate
else
sys+=rot.move( sol.size() ); // rotate
if (slp_global()<0.5)
dian.sampleMuCorrelationAndKirkwood(spc);
if (slp_global()>0.99)
xtc.save(textio::prefix+"out.xtc", spc.p);
dian.sampleDP(spc);
}
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing() << std::flush;
}
// perform unit tests
trans.test(test);
rot.test(test);
sys.test(test);
sdp.saveDipoleWRL("stockmayer.wrl",spc,sol);
FormatPQR().save("confout.pqr", spc.p);
std::cout << spc.info() + pot.info() + trans.info()
+ rot.info() + sys.info() + test.info() + dian.info(); // final info
dian.save();
spc.save("state");
return test.numFailed();
}
int main() {
InputMap mcp("grand.json"); // open user input file
Tspace spc(mcp); // simulation space
Energy::Nonbonded<Tspace,CoulombHS> pot(mcp); // hamiltonian
pot.setSpace(spc); // share space w. hamiltonian
spc.load("state",Tspace::RESIZE); // load old config. from disk (if any)
// Two different Widom analysis methods
double lB = pot.pairpot.first.bjerrumLength();// get bjerrum length
Analysis::Widom<PointParticle> widom1; // widom analysis (I)
Analysis::WidomScaled<Tspace> widom2(lB,1); // ...and (II)
widom1.add(spc.p);
widom2.add(spc.p);
Move::Propagator<Tspace> mv(mcp,pot,spc);
EnergyDrift sys; // class for tracking system energy drifts
sys.init(Energy::systemEnergy(spc,pot,spc.p));// store initial total system energy
cout << atom.info() + spc.info() + pot.info() + "\n";
MCLoop loop(mcp); // class for handling mc loops
while ( loop[0] ) {
while ( loop[1] ) {
sys+=mv.move(); // move!
widom1.sample(spc,pot,1);
widom2.sample(spc.p,spc.geo);
} // end of micro loop
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // calc. energy drift
cout << loop.timing();
} // end of macro loop
FormatPQR::save("confout.pqr", spc.p); // PQR snapshot for VMD etc.
spc.save("state"); // final simulation state
UnitTest test(mcp); // class for unit testing
mv.test(test);
sys.test(test);
widom1.test(test);
cout << loop.info() + sys.info() + mv.info() + test.info()
+ widom1.info() + widom2.info();
return test.numFailed();
}
int main() {
InputMap mcp("gcmol.input"); // open user input file
MCLoop loop(mcp); // class for handling mc loops
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp);
// Create Space and a Hamiltonian with three terms
Tspace spc(mcp);
auto pot = Energy::Nonbonded<Tspace,Tpairpot>(mcp);
// ADD CONFIGURATIONS FOR POOL INSERTS
string file = mcp.get<string>("polymer_file", "");
p_vec conf;
FormatAAM::load(file,conf);
molecule.pushConfiguration("polymer", conf); // p_vec is one molecule large
molecule.pushConfiguration("polymer2",conf);
// Markov moves and analysis
Move::GCMolecular<Tspace> gc(mcp, pot, spc);
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // store initial total system energy
cout << atom.info() << molecule.info() << gc.info() << spc.info() << pot.info() << textio::header("MC Simulation Begins!");
while ( loop[0] ) { // Markov chain
while ( loop[1] ) {
sys+=gc.move();
}
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing();
} // end of macro loop
sys.test(test);
gc.test(test);
// print information
cout << loop.info() << sys.info() << gc.info() << spc.info() <<test.info() << endl;
// clean allocated memory
spc.freeGroups();
return test.numFailed();
}
int main() {
cout << textio::splash(); // show faunus banner and credits
InputMap mcp("membrane.json"); //read input file
FormatXTC xtc(1000);
EnergyDrift sys; // class for tracking system energy drifts
// Energy functions and space
auto pot = Energy::NonbondedCutg2g<Tspace,Tpairpot>(mcp)
+ Energy::Bonded<Tspace>()
+ Energy::ExternalPressure<Tspace>(mcp)
+ Energy::EquilibriumEnergy<Tspace>(mcp);
auto nonbonded = std::get<0>( pot.tuple() );
auto bonded = std::get<1>( pot.tuple() );
nonbonded->noPairPotentialCutoff=true;
Tspace spc(mcp);
auto lipids = spc.findMolecules("lipid");
Group allLipids( lipids.front()->front(), lipids.back()->back() );
allLipids.setMolSize(3);
MakeDesernoMembrane(allLipids, *bonded, nonbonded->pairpot, mcp);
// Place all lipids in xy plane (z=0);
for ( auto g : lipids ) {
double dz = spc.p[ g->back() ].z();
for (auto i : *g) {
spc.p[i].z() -= dz;
spc.geo.boundary( spc.p[i] );
}
g->setMassCenters( spc );
}
spc.trial=spc.p; // sync. particle trial vector
spc.load("state"); // load old config. from disk (if any)
// Markov moves and analysis
Move::Propagator<Tspace> mv(mcp, pot, spc);
Analysis::BilayerStructure lipidstruct;
Analysis::VirialPressure<Tspace> virial(mcp, pot, spc);
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // store total energy
cout << atom.info() + spc.info() + pot.info();
MCLoop loop(mcp); // class for handling mc loops
while ( loop[0] ) { // Markov chain
while ( loop[1] ) {
sys += mv.move();
double ran = slump();
if ( ran > 0.99 ) {
xtc.setbox( spc.geo.len );
xtc.save("traj.xtc", spc.p);
}
if ( ran > 0.90 ) {
virial.sample();
lipidstruct.sample(spc.geo, spc.p, allLipids);
}
} // end of micro loop
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // energy drift?
// save to disk
FormatPQR::save("confout.pqr", spc.p);
spc.save("state");
cout << loop.timing();
} // end of macro loop
// perform unit tests
UnitTest test(mcp);
mv.test(test);
sys.test(test);
lipidstruct.test(test);
cout << loop.info() + mv.info()
+ lipidstruct.info() + sys.info() + virial.info() + test.info();
return test.numFailed();
}
int main() {
std::vector<Coord> sasaCoords; //vector of sasa coordinates
std::vector<Scalar> sasaWeights; //vector of sasa weights
clock_t clk_a, clk_b, clk_sum = 0;
/*
sasaCoords.push_back(Coord(1.0,2.0,3.0));
sasaWeights.push_back(1.0);
POWERSASA::PowerSasa<Scalar,Coord> *ps =
new POWERSASA::PowerSasa<Scalar,Coord>(sasaCoords, sasaWeights, 1, 1, 1, 1);
ps->calc_sasa_all();
Scalar volume = 0.0, surf = 0.0;
for (unsigned int i = 0; i < sasaCoords.size(); ++i)
{
printf("%4d sasa=%7.3lf vol=%7.3lf\n", i, (ps->getSasa())[i], (ps->getVol())[i]);
volume += (ps->getVol())[i];
surf += (ps->getSasa())[i];
}
printf("volume=%lf\n", volume);
printf("sasa =%lf\n", surf);
delete ps;
*/
cout << textio::splash(); // show faunus banner and credits
InputMap mcp("polymers.input"); // open user input file
MCLoop loop(mcp); // class for handling mc loops
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp); // class for unit testing
// Create Space and a Hamiltonian with three terms
Tspace spc(mcp);
auto pot = Energy::Nonbonded<Tspace,Tpairpot>(mcp)
+ Energy::SASAEnergy<Tspace>(mcp)
+ Energy::ExternalPressure<Tspace>(mcp) + Energy::Bonded<Tspace>();
auto bonded = &pot.second; // pointer to bond energy class
// Add salt
Group salt;
salt.addParticles(spc, mcp);
// Add polymers
vector<Group> pol( mcp.get("polymer_N",0)); // vector of polymers
string file = mcp.get<string>("polymer_file", "");
double req = mcp.get<double>("polymer_eqdist", 0);
double k = mcp.get<double>("polymer_forceconst", 0);
for (auto &g : pol) { // load polymers
Tspace::ParticleVector v; // temporary, empty particle vector
FormatAAM::load(file,v); // load AAM structure into v
Geometry::FindSpace().find(spc.geo,spc.p,v); // find empty spot in particle vector
g = spc.insert(v); // insert into space
g.name="Polymer";
spc.enroll(g);
for (int i=g.front(); i<g.back(); i++)
bonded->add(i, i+1, Potential::Harmonic(k,req)); // add bonds
}
Group allpol( pol.front().front(), pol.back().back() );// make group w. all polymers
// Markov moves and analysis
Move::Isobaric<Tspace> iso(mcp,pot,spc);
Move::TranslateRotate<Tspace> gmv(mcp,pot,spc);
Move::AtomicTranslation<Tspace> mv(mcp, pot, spc);
Move::CrankShaft<Tspace> crank(mcp, pot, spc);
Move::Pivot<Tspace> pivot(mcp, pot, spc);
Analysis::PolymerShape shape;
Analysis::RadialDistribution<> rdf(0.2);
Scatter::DebyeFormula<Scatter::FormFactorUnity<>> debye(mcp);
spc.load("state"); // load old config. from disk (if any)
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // store initial total system energy
cout << atom.info() << spc.info() << pot.info() << textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int k,i=slp_global.rand() % 6;
switch (i) {
case 0:
mv.setGroup(salt);
sys+=mv.move( salt.size() ); // translate salt
break;
case 1:
mv.setGroup(allpol);
sys+=mv.move( allpol.size() );// translate monomers
for (auto &g : pol) {
g.setMassCenter(spc);
shape.sample(g,spc); // sample gyration radii etc.
}
break;
case 2:
k=pol.size();
while (k-->0) {
gmv.setGroup( pol[ slp_global.rand() % pol.size() ] );
sys+=gmv.move(); // translate/rotate polymers
}
break;
case 3:
sys+=iso.move(); // isobaric volume move
break;
case 4:
k=pol.size();
while (k-->0) {
crank.setGroup( pol[ slp_global.rand() % pol.size() ] );
sys+=crank.move(); // crank shaft move
}
break;
case 5:
k=pol.size();
while (k-->0) {
pivot.setGroup( pol[ slp_global.rand() % pol.size() ] );
sys+=pivot.move(); // pivot move
}
break;
}
// polymer-polymer mass center rdf
for (auto i=pol.begin(); i!=pol.end()-1; i++)
for (auto j=i+1; j!=pol.end(); j++)
rdf( spc.geo.dist(i->cm,j->cm) )++;
// SASA
sasaCoords.clear();
sasaWeights.clear();
/*
for (auto i = pol.begin(); i != pol.end(); i++) {
sasaCoords.push_back(i->cm);
sasaWeights.push_back(5.0);
}
*/
/*
for (auto i = allpol.begin(); i != allpol.end(); i++) {
auto monomer = spc.p.at(*i);
sasaCoords.push_back(monomer);
sasaWeights.push_back(10.0);
}
clk_a = clock();
auto ps = new POWERSASA::PowerSasa<Scalar,Coord>(sasaCoords, sasaWeights, 1, 1, 1, 1);
ps->calc_sasa_all();
clk_b = clock();
clk_sum += clk_b - clk_a;
{
Scalar volume = 0.0, surf = 0.0;
for (unsigned int i = 0; i < sasaCoords.size(); ++i)
{
volume += (ps->getVol())[i];
surf += (ps->getSasa())[i];
}
//printf("volume=%lf\n", volume);
//printf("sasa =%lf\n", surf);
}
delete ps;
*/
} // end of micro loop
// sample scattering
debye.sample(spc.p);
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing();
} // end of macro loop
// save to disk
rdf.save("rdf_p2p.dat");
spc.save("state");
debye.save("debye.dat");
FormatPQR::save("confout.pqr", spc.p);
// perform unit tests
iso.test(test);
gmv.test(test);
mv.test(test);
sys.test(test);
// print information
cout << loop.info() << sys.info() << mv.info() << gmv.info() << crank.info()
<< pivot.info() << iso.info() << shape.info() << test.info();
cout << endl << endl << "SASA" << endl;
cout << "Time " << (float) clk_sum/CLOCKS_PER_SEC << " s = " << (float) clk_sum/CLOCKS_PER_SEC/3600 << " h" << endl;
cout << sasaCoords.size() << endl;
cout << pot.first.first.second.info() ;
/*
cout << allpol.size() << endl;
cout << allpol.info() << endl;
cout << spc.info() << endl;
cout << typeid(spc.p.at(34)).name() << endl;
cout << typeid(allpol.begin()).name() << endl;
cout << spc.findGroup(34)->info() << endl;
*/
//for (auto i = allpol.begin(); i != allpol.end(); i++) {
//}
return test.numFailed();
}
int main() {
cout << textio::splash(); // Spam
InputMap mcp("slitpolymer.input"); // Open input parameter file
MCLoop loop(mcp); // handle mc loops
EnergyDrift sys; // track system energy drifts
UnitTest test(mcp); // unit testing
Geometry::Cuboidslit geo(mcp); // rectangular simulation box w. XY periodicity
Energy::ExternalPotential< Potential::GouyChapman<> > pot(mcp);
pot.setGeometry(geo); // Pass on geometry to potential
pot.expot.setSurfPositionZ( &geo.len_half.z() ); // Pass position of GC surface
Space spc( pot.getGeometry() ); // Simulation space (all particles and group info)
// Load and add polymer to Space
FormatAAM aam; // AAM structure file I/O
string polyfile = mcp.get<string>("polymer_file", "");
aam.load(polyfile); // Load polymer structure into aam class
Geometry::FindSpace().find(*spc.geo, spc.p, aam.particles()); // find empty spot
GroupMolecular pol = spc.insert( aam.particles() ); // Insert into Space and return matching group
pol.name="polymer"; // Give polymer arbitrary name
spc.enroll(pol); // Enroll polymer in Space
// MC moves
Move::TranslateRotate gmv(mcp,pot,spc);
Move::CrankShaft crank(mcp,pot,spc);
Move::Pivot pivot(mcp,pot,spc);
Move::Reptation rep(mcp,pot,spc);
Analysis::PolymerShape shape; // sample polymer shape
Analysis::LineDistribution<> surfmapall; // monomer-surface histogram
spc.load("state"); // Load start configuration, if any
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // Store total system energy
cout << spc.info() + pot.info() + pol.info() + textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int i=slp_global.rand() % 4;
switch (i) {
case 0: // translate and rotate polymer
gmv.setGroup(pol);
sys+=gmv.move();
break;
case 1: // pivot
pivot.setGroup(pol);
sys+=pivot.move();
break;
case 2: // crankshaft
crank.setGroup(pol);
sys+=crank.move();
break;
case 3: // reptation
rep.setGroup(pol);
sys+=rep.move();
break;
}
double rnd = slp_global(); // [0:1[
if (rnd<0.05)
shape.sample(pol,spc); // sample polymer shape - gyration radius etc.
if (rnd<0.05)
for (auto i : pol)
surfmapall( pot.expot.surfDist( spc.p[i] ) )++; // sample monomer distribution
} // end of micro loop
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) ); // re-calc system energy and detect drift
cout << loop.timing(); // print timing and ETA information
} // end of macro loop
spc.save("state"); // save final state of simulation (positions etc)
surfmapall.save("surfall.dat"); // save monomer-surface distribution
FormatPQR().save("confout.pqr", spc.p); // save PQR file
// Perform unit tests (only for faunus integrity)
gmv.test(test);
sys.test(test);
pivot.test(test);
crank.test(test);
rep.test(test);
shape.test(test);
cout << loop.info() + sys.info() + gmv.info() + crank.info()
+ pivot.info() + rep.info() + shape.info() + spc.info() + test.info();
return test.numFailed();
}
