int main() {
cout << textio::splash();
InputMap mcp("cigars2fibrils.json");
FormatMXYZ mxyz;
EnergyDrift sys;
// Energy functions and space
Tspace spc(mcp);
Energy::NonbondedVector<Tspace,Tpairpot> pot(mcp);
// Markov moves and analysis
Move::Propagator<Tspace> mv( mcp, pot, spc );
sys.init( Energy::systemEnergy( spc,pot,spc.p ) );
cout << atom.info() + spc.info() + pot.info() + textio::header("MC Simulation Begins!");
MCLoop loop( mcp );
mxyz.save( "cigars2fibrils-mov", spc.p, spc.geo.len, loop.innerCount() );
while ( loop[0] ) { // Markov chain
while ( loop[1] )
sys += mv.move();
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing();
mxyz.save( "cigars2fibrils-mov", spc.p, spc.geo.len, loop.innerCount() );
} // end of macro loop
// print information about simulationat the end
cout << loop.info() + sys.info() + mv.info();
}
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() {
cout << textio::splash(); // show faunus banner and credits
//InputMap mcp("cigars2fibrils.input"); // open user input file
InputMap mcp("psc-nvt.input");
MCLoop loop(mcp); // class for handling mc loops
FormatMXYZ mxyz; // MXYZ structure file I/O
EnergyDrift sys; // class for tracking system energy drifts
// Energy functions and space
Tspace spc(mcp);
auto pot = Energy::NonbondedVector<Tspace,Tpairpot>(mcp);
// Markov moves and analysis
Move::AtomicTranslation<Tspace> mv(mcp, pot, spc);
Move::AtomicRotation<Tspace> rot(mcp, pot, spc);
cout <<"before adding cigars";
// Add cigars
Group cigars;
cigars.addParticles(spc, mcp);
cigars.name="PSC";
for (auto i : cigars) {
spc.p[i].dir.ranunit(slump);
spc.p[i].patchdir.ranunit(slump);
Geometry::cigar_initialize(spc.geo, spc.p[i]);
spc.trial[i]=spc.p[i];
}
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!");
mxyz.save("cigars2fibrils-mov", spc.p, spc.geo.len, loop.count());
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int i= slump.rand() % 2;
switch (i) {
case 0:
mv.setGroup(cigars);
sys+=mv.move( cigars.size() ); // translate cigars
break;
case 1:
rot.setGroup(cigars);
sys+=rot.move( cigars.size() ); // translate cigars
break;
}
} // end of micro loop
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing();
mxyz.save("cigars2fibrils-mov", spc.p, spc.geo.len, loop.count());
} // end of macro loop
// print information
cout << loop.info() << sys.info() << mv.info() << rot.info();
}
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<Tpair,Tgeo> pot(in); // create Hamiltonian, non-bonded only
EnergyDrift sys; // class for tracking system energy drifts
Space spc( pot.getGeometry() ); // create simulation space, particles etc.
GroupAtomic sol(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(0.05); // particle-particle g(r)
Move::AtomicTranslation trans(in, pot, spc); // particle move class
Move::AtomicRotation rot(in, pot, spc); // particle move class
//PolarizeMove<AtomicTranslation> trans(in,pot,spc);
//PolarizeMove<AtomicRotation> 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_ST");
double limit = 1e-6;
Point ExternalField(0,0,0);
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // store initial total system 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()<0.5)
for (auto i=sol.front(); i<sol.back(); i++) { // salt radial distribution function
for (auto j=i+1; j<=sol.back(); j++) {
double r =pot.geometry.dist(spc.p[i],spc.p[j]);
rdf(r)++;
mucorr(r) += spc.p[i].mu.dot(spc.p[j].mu)/(spc.p[i].muscalar*spc.p[j].muscalar);
}
}
}
cout << "Eps: " << getDielectricConstant(pot,spc,in.get<double>("dipdip_cutoff",pc::infty)) << "\n";
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // compare energy sum with current
cout << loop.timing();
}
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(); // final info
spc.save("state_ST");
}
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() {
cout << textio::splash(); // faunus splash info!
::atom.includefile("titrate.json"); // load atom properties
InputMap mcp("titrate.input");
EnergyDrift sys; // track system energy drift
UnitTest test(mcp);
// Space and hamiltonian
Tspace spc(mcp);
auto pot = Energy::Nonbonded<Tspace,Potential::DebyeHuckel>(mcp)
+ Energy::EquilibriumEnergy<Tspace>(mcp);
// Add molecule to middle of simulation container
string file = mcp.get<string>("molecule", string());
Tspace::ParticleVector v;
FormatAAM::load(file,v);
Geometry::cm2origo(spc.geo,v); // center molecule
Group g = spc.insert(v); // insert into space
g.name="peptide"; // babtise
spc.enroll(g); // enroll group in space
spc.load("state");
Move::SwapMove<Tspace> tit(mcp,pot,spc,pot.second);
Analysis::ChargeMultipole mp;
sys.init( Energy::systemEnergy(spc,pot,spc.p) );
cout << atom.info() + spc.info() + pot.info() + tit.info()
+ textio::header("MC Simulation Begins!");
MCLoop loop(mcp); // class for handling mc loops
while ( loop[0] ) { // Markov chain
while ( loop[1] ) {
sys+=tit.move();
mp.sample(g,spc);
} // end of micro loop
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) );
cout << loop.timing();
} // end of macro loop
cout << loop.info() + sys.info() + tit.info() + g.info() + mp.info();
FormatPQR().save("confout.pqr", spc.p);
spc.save("state");
}
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(int argc, char** argv) {
InputMap mcp("cyl.input");
MCLoop loop(mcp); // class for handling mc loops
FormatXTC xtc(1000); // XTC gromacs trajectory format
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp);
bool movie = mcp.get("movie", true);
Tspace spc(mcp);
auto pot = Energy::Nonbonded<Tspace,Tpairpot>(mcp)
+ Energy::ExternalPressure<Tspace>(mcp)
+ Energy::HydrophobicSASA<Tspace>(mcp)
+ Energy::EquilibriumEnergy<Tspace>(mcp);
auto eqenergy = &pot.second;
// set hydrophobic-hydrophobic LJ epsilon
double epsh = mcp.get("eps_hydrophobic", 0.05);
for (size_t i=0; i<atom.size()-1; i++)
for (size_t j=i+1; j<atom.size(); j++)
if (atom[i].hydrophobic)
if (atom[j].hydrophobic)
pot.first.first.first.pairpot.second.customEpsilon(i,j,epsh);
// Add molecules
int N1 = mcp.get("molecule1_N",0);
int N2 = mcp.get("molecule2_N",0);
bool inPlane = mcp.get("molecule_plane", false);
string file;
vector<Group> pol(N1+N2);
for (int i=0; i<N1+N2; i++) {
if (i>=N1)
file = mcp.get<string>("molecule2");
else
file = mcp.get<string>("molecule1");
Tspace::ParticleVector v;
// PQR or AAM molecular file format?
if (file.find(".pqr")!=std::string::npos)
FormatPQR::load(file,v);
else
FormatAAM::load(file,v);
Geometry::FindSpace fs;
if (inPlane)
fs.dir=Point(0,0,1);
fs.find(spc.geo,spc.p,v);
pol[i] = spc.insert(v);
pol[i].name=file+std::to_string(i);
spc.enroll( pol[i] );
}
Group allpol( pol.front().front(), pol.back().back() );
// Add atomic species
Group salt;
salt.addParticles(spc, mcp);
salt.name="Atomic Species";
spc.enroll(salt);
Analysis::LineDistribution<> rdf(0.5);
Analysis::ChargeMultipole mpol;
Analysis::MultipoleDistribution<Tspace> mpoldist(mcp);
FormatQtraj qtrj("qtrj.dat");
spc.load("state");
Move::Isobaric<Tspace> iso(mcp,pot,spc);
Move::TranslateRotate<Tspace> gmv(mcp,pot,spc);
Move::AtomicTranslation<Tspace> mv(mcp, pot, spc);
Move::SwapMove<Tspace> tit(mcp,pot,spc,*eqenergy);
if (inPlane)
for (auto &m : pol)
gmv.directions[ m.name ]=Point(0,0,1);
eqenergy->eq.findSites(spc.p);
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // Store total system energy
cout << atom.info() << spc.info() << pot.info() << tit.info()
<< textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int k,i=rand() % 2;
switch (i) {
case 0:
k=pol.size();
while (k-->0) {
gmv.setGroup( pol[ rand() % pol.size() ] );
sys+=gmv.move();
}
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) )++;
break;
case 1:
sys+=tit.move();
break;
case 2:
sys+=iso.move();
break;
case 3:
mv.setGroup(salt);
sys+=mv.move();
break;
}
double xi = slp_global(); // random number [0,1)
// Sample multipolar moments and distribution
if ( xi>0.95 ) {
pol[0].setMassCenter(spc);
pol[1].setMassCenter(spc);
mpol.sample(pol,spc);
mpoldist.sample(spc, pol[0], pol[1]);
}
if ( movie==true && xi>0.995 ) {
xtc.setbox( 1000. );
xtc.save("traj.xtc", spc.p);
qtrj.save(spc.p);
}
} // end of micro loop
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) ); // detect energy drift
cout << loop.timing();
spc.save("state");
mcp.save("mdout.mdp");
rdf.save("rdf_p2p.dat");
mpoldist.save("multipole.dat");
FormatPQR::save("confout.pqr", spc.p);
} // end of macro loop
cout << loop.info() + sys.info() + gmv.info() + mv.info()
+ iso.info() + tit.info() + mpol.info();
}
int main(int argc, char** argv) {
cout << textio::splash();
InputMap mcp("cluster.input");
MCLoop loop(mcp); // class for handling mc loops
FormatPQR pqr; // PQR structure file I/O
FormatAAM aam; // AAM structure file I/O
FormatXTC xtc(1000); // XTC gromacs trajectory format
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp);
Energy::Hamiltonian pot;
#ifdef tab
Energy::Nonbonded<Potential::PotentialMapTabulated<Tpairpot,Tabulate::tabulator<double>>,Tgeometry> nb(mcp); // Tabulation
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef tablin
Energy::Nonbonded<Potential::PotentialMapTabulated<Tpairpot,Tabulate::tabulatorlin<double>>,Tgeometry> nb(mcp); // Tabulation
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef tabherm
Energy::Nonbonded<Potential::PotentialMapTabulated<Tpairpot,Tabulate::tabulatorherm<double>>,Tgeometry> nb(mcp); // Tabulation
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef tabopt
Energy::Nonbonded<Potential::PotentialVecTabulated<Tpairpot,Tabulate::tabulator<double>>,Tgeometry> nb(mcp); // Tabulation optimized
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef taboptlin
Energy::Nonbonded<Potential::PotentialVecTabulated<Tpairpot,Tabulate::tabulatorlin<double>>,Tgeometry> nb(mcp); // Tabulation optimized
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef taboptherm
Energy::Nonbonded<Potential::PotentialVecTabulated<Tpairpot,Tabulate::tabulatorherm<double>>,Tgeometry> nb(mcp); // Tabulation optimized
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef org
Energy::Nonbonded<Potential::PotentialMap<Tpairpot>,Tgeometry> nb(mcp); // Non-tabulation
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef orgopt
Energy::Nonbonded<Potential::PotentialVec<Tpairpot>,Tgeometry> nb(mcp); // Non-tabulation
nb.pairpot.add(atom["Ca"].id,atom["Ca"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Ca"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Na"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Na"].id,atom["Cl"].id,Tpairpot(mcp));
nb.pairpot.add(atom["Cl"].id,atom["Cl"].id,Tpairpot(mcp));
auto nonbonded = pot.create(nb);
#endif
#ifdef tabsingle
auto nonbonded = pot.create( Energy::Nonbonded<Potential::PotentialTabulate<Tpairpot>,Tgeometry>(mcp) );
#endif
#ifdef taboptsingle
auto nonbonded = pot.create( Energy::Nonbonded<Potential::PotentialTabulateVec<Tpairpot>,Tgeometry>(mcp) );
#endif
#ifdef orgsingle
auto nonbonded = pot.create( Energy::Nonbonded<Tpairpot,Tgeometry>(mcp) );
#endif
//nb.pairpot.print_tabulation(); // Print files to compare tabulation with real potential
Space spc( pot.getGeometry() );
// Add salt
GroupAtomic salt(spc, mcp);
salt.name="Salt";
spc.enroll(salt);
spc.load("state");
Move::AtomicTranslation mv(mcp, pot, spc);
mv.setGroup(salt); // specify atomic particles to be moved
short na = atom["Na"].id;
short ca = atom["Ca"].id;
short cl = atom["Cl"].id;
Analysis::RadialDistribution<float,unsigned int> rdf1(0.2); // 0.2 Å resolution
Analysis::RadialDistribution<float,unsigned int> rdf2(0.2); // 0.2 Å resolution
sys.init( Energy::systemEnergy(spc,pot,spc.p) );
cout << atom.info() << spc.info() << pot.info() << textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
xtc.save("out.xtc", spc.p);
int i=rand() % 1;
switch (i) {
case 0:
mv.setGroup(salt);
sys+=mv.move( salt.size()/2+1 );
break;
}
if (slp_global() > 0.9) {
rdf1.sample( spc, salt, na, cl );
rdf2.sample( spc, salt, ca, cl );
}
} // end of micro loop
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) );
spc.save("state");
cout << loop.timing();
} // end of macro loop
#ifdef tab
rdf1.save("naclrdf_tab.dat");
rdf2.save("caclrdf_tab.dat");
#endif
#ifdef tabopt
rdf1.save("naclrdf_tabopt.dat");
rdf2.save("caclrdf_tabopt.dat");
#endif
#ifdef org
rdf1.save("naclrdf_notab.dat");
rdf2.save("caclrdf_notab.dat");
#endif
pqr.save("confout.pqr", spc.p);
cout << loop.info() << spc.info() << sys.info() << mv.info();
}
int main(int argc, char** argv) {
InputMap mcp("cyl.input");
MCLoop loop(mcp); // class for handling mc loops
FormatXTC xtc(1000); // XTC gromacs trajectory format
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp);
bool inPlane = mcp.get<bool>("molecule_plane");
Tspace spc(mcp);
auto pot = Energy::Nonbonded<Tspace,Tpairpot>(mcp)
+ Energy::MassCenterConstrain<Tspace>(mcp)
+ Energy::EquilibriumEnergy<Tspace>(mcp);
auto constrainenergy = &pot.first.second;
auto eqenergy = &pot.second;
// Add molecules
int N1 = mcp.get("molecule1_N",0);
int N2 = mcp.get("molecule2_N",0);
string file;
vector<Group> pol(N1+N2);
for (int i=0; i<N1+N2; i++) {
if (i>=N1)
file = mcp.get<string>("molecule2");
else
file = mcp.get<string>("molecule1");
Tspace::ParticleVector v;
FormatAAM::load(file,v);
Geometry::FindSpace fs;
if (inPlane)
fs.dir=Point(0,0,1);
fs.find(spc.geo,spc.p,v);
pol[i] = spc.insert(v);
pol[i].name=file+std::to_string(i);
spc.enroll( pol[i] );
}
Group allpol( pol.front().front(), pol.back().back() );
constrainenergy->addPair(pol[0], pol[1]);
// Add atomic species
Group salt;
salt.addParticles(spc, mcp);
salt.name="Atomic Species";
spc.enroll(salt);
Analysis::LineDistribution<> rdf(0.5);
Analysis::ChargeMultipole mpol;
spc.load("state");
Move::Isobaric<Tspace> iso(mcp,pot,spc);
Move::TranslateRotate<Tspace> gmv(mcp,pot,spc);
Move::AtomicTranslation<Tspace> mv(mcp, pot, spc);
Move::SwapMove<Tspace> tit(mcp,pot,spc,*eqenergy);
if (inPlane)
for (auto &m : pol)
gmv.directions[ m.name ]=Point(0,0,1);
eqenergy->eq.findSites(spc.p);
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // Store total system energy
cout << atom.info() << spc.info() << pot.info() << tit.info()
<< textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int k,i=rand() % 2;
switch (i) {
case 0:
k=pol.size();
while (k-->0) {
gmv.setGroup( pol[ rand() % pol.size() ] );
sys+=gmv.move();
}
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) )++;
break;
case 1:
sys+=tit.move();
if( slp_global()>0.9 )
mpol.sample(pol,spc);
break;
case 2:
sys+=iso.move();
break;
case 3:
mv.setGroup(salt);
sys+=mv.move();
break;
}
if ( slp_global()<-0.001 ) {
xtc.setbox( 1000. );
xtc.save("traj.xtc", spc);
}
} // end of micro loop
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) ); // detect energy drift
cout << loop.timing();
rdf.save("rdf_p2p_macro" + std::to_string(loop.getMacroCnt()) +".dat");
FormatPQR::save("confout.pqr", spc.p);
spc.save("state");
mcp.save("mdout.mdp");
} // end of macro loop
cout << loop.info() + sys.info() + gmv.info() + mv.info()
+ iso.info() + tit.info() + mpol.info();
}
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();
}
int main(int argc, char** argv) {
Faunus::MPI::MPIController mpi;
InputMap mcp(textio::prefix+"input");
mpi.cout << textio::splash();
MCLoop loop(mcp); // class for handling mc loops
FormatPQR pqr; // PQR structure file I/O
FormatAAM aam; // AAM structure file I/O
FormatTopology top;
FormatXTC xtc(1000); // XTC gromacs trajectory format
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp);
Energy::Hamiltonian pot;
auto nonbonded = pot.create( Energy::Nonbonded<Tpairpot,Tgeometry>(mcp) );
//auto constrain = pot.create( Energy::MassCenterConstrain(pot.getGeometry()) );
Space spc( pot.getGeometry() );
// Add molecular species
int cnt=0;
int N1=mcp.get("polymer1_N",0);
int N2=mcp.get("polymer2_N",0);
vector<GroupMolecular> pol( N1+N2);
for (auto &g : pol) {
cnt++;
string polyfilekey = (cnt>N1) ? "polymer2_file" : "polymer1_file";
aam.load( mcp.get<string>(polyfilekey, "") );
Geometry::FindSpace f;
f.dir.x()=0; // put mass center
f.dir.y()=0; // at [x,y,z] = [0,0,random]
if (f.find(*spc.geo, spc.p, aam.p )) {
g = spc.insert( aam.p );
g.name=mcp.get<string>(polyfilekey, "");
spc.enroll(g);
} else
return 1;
}
//constrain->addPair(pol[0], pol[1], 20, 150);
// Add salt
GroupAtomic salt(spc, mcp);
salt.name="Salt";
//spc.enroll(salt);
Move::SwapMove tit(mcp,pot,spc);
Move::TranslateRotate gmv(mcp,pot,spc);
Move::AtomicTranslation mv(mcp, pot, spc);
Move::ParallelTempering pt(mcp,pot,spc,mpi);
mv.setGroup(salt); // specify atomic particles to be moved
tit.findSites(spc.p); // search for titratable sites
spc.load(textio::prefix+"state");
typedef Analysis::Table2D<float, Average<double> > Tdiptable;
Tdiptable dip1(0.25, Tdiptable::XYDATA);
Tdiptable dip2(0.25, Tdiptable::XYDATA);
Tdiptable dipdip(0.25, Tdiptable::XYDATA);
gmv.directions[ pol[0].name ].x()=0; // do not move in x
gmv.directions[ pol[0].name ].y()=0; // do not move in y
gmv.directions[ pol[0].name ].z()=1; // do move in z
gmv.directions[ pol[1].name ].x()=0; // do not move in x
gmv.directions[ pol[1].name ].y()=0; // do not move in y
gmv.directions[ pol[1].name ].z()=1; // do move in z
Analysis::LineDistribution<float,unsigned long int> rdf(0.5);
//rdf.maxdist=150;
sys.init( Energy::systemEnergy(spc,pot,spc.p) );
mpi.cout << atom.info() << spc.info() << pot.info() << textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int k,i=rand() % 3;
switch (i) {
case 2:
sys+=pt.move();
//mv.setGroup(salt);
//sys+=mv.move( salt.size()/2 );
break;
case 0:
if (slp_global()<0.1)
sys+=tit.move();
break;
case 1:
k=pol.size();
while (k-->0) {
gmv.setGroup( pol[ rand() % pol.size() ] );
sys+=gmv.move();
}
for (auto i=pol.begin(); i!=pol.end()-1; i++)
for (auto j=i+1; j!=pol.end(); j++) {
double r=spc.geo->dist(i->cm,j->cm);
if (r<rdf.maxdist) {
rdf(r)++;
}
}
double r=spc.geo->dist(pol[0].cm,pol[1].cm);
Point mu1 = pol[0].dipolemoment(spc);
Point mu2 = pol[1].dipolemoment(spc);
dip1(r) += mu1.z()/mu1.len();
dip2(r) += mu2.z()/mu2.len();
dipdip(r) += mu1.z()*mu2.z() / mu1.len() / mu2.len();
break;
}
} // end of micro loop
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) );
rdf.save(textio::prefix+"rdf_p2p.dat");
mpi.cout << loop.timing();
} // end of macro loop
pqr.save(textio::prefix+"confout.pqr", spc.p);
spc.save(textio::prefix+"state");
dip1.save(textio::prefix+"dip1.dat");
dip2.save(textio::prefix+"dip2.dat");
dipdip.save(textio::prefix+"dipdip.dat");
mpi.cout << loop.info() << spc.info() << sys.info() << mv.info() << gmv.info()
<< tit.info() << pol[0].info() << pol[0].charge(spc.p) << pt.info();
}
int main(int argc, char** argv) {
Faunus::MPI::MPIController mpi;
mpi.cout << textio::splash();
InputMap mcp(textio::prefix+"manybody.input");
MCLoop loop(mcp); // class for handling mc loops
FormatPQR pqr; // PQR structure file I/O
FormatAAM aam; // AAM structure file I/O
FormatTopology top;
FormatXTC xtc(1000); // XTC gromacs trajectory format for only cuboid geomtries
EnergyDrift sys; // class for tracking system energy drifts
UnitTest test(mcp);
Energy::Hamiltonian pot;
auto nonbonded = pot.create( Energy::Nonbonded<Tpairpot,Tgeometry>(mcp) );
auto bonded = pot.create( Energy::Bonded() );
// auto mfc = pot.create( Energy::MeanFieldCorrection(mcp) ); //pot.create returns a smart pointer!!
auto swpair = pot.create( Energy::PairListID() );
swpair->add( atom["HIS"].id, atom["Zn"].id, Potential::SquareWell(mcp) ); //add square-well poteintial between Zn+2 and HIS resiues
swpair->add( atom["ZNHIS"].id, atom["HIS"].id, Potential::SquareWellShifted(mcp, "squarewell_ZNHIS") ); //add square-well poteintial between ZNHIS and HIS resiues
#ifdef SLIT
auto gouy = pot.create( Energy::GouyChapman(mcp) );
gouy->setPosition( nonbonded->geometry.len_half.z() ); // Place the surface xy plane at +z direction
auto restricted = pot.create( Energy::RestrictedVolumeCM(mcp) );
#endif
Space spc( pot.getGeometry() );
// Add polymers
vector<GroupMolecular> pol( mcp.get("polymer_N",0) );
string polyfile = mcp.get<string>("polymer_file", "");
atom["MM"].dp = 0.;
int ii=1;
mpi.cout << "Number of polymers: " << pol.size() << endl;
for (auto &g : pol) { // load polymers
aam.load(polyfile);
Geometry::FindSpace f;
f.find(*spc.geo, spc.p, aam.particles()); // find empty spot in particle vector
g = spc.insert( aam.particles() ); // insert into space
ostringstream o;
o << "Polymer" << ii++;
g.name=o.str();
spc.enroll(g);
#ifdef SLIT
//(*restricted).groups.push_back( &g ); // Restrict center of masses of all proteins
restricted->groups.push_back( &g ); // Restrict center of masses of all proteins
#endif
for (int i=g.front(); i<g.back(); i++)
bonded->add(i, i+1, Tbondpot(mcp, "polymer_", "minuslj_")); // add bonds
}
Group allpol( pol.front().front(), pol.back().back() ); // make group w. all polymers
// Add salts
GroupAtomic salt(spc, mcp);
salt.name="salt";
mpi.cout << "Number of salts: " << salt.size() << endl;
// atom["NTR"].dp = 10.;
// atom["CTR"].dp = 10.;
// atom["HIS"].dp = 10.;
// atom["HNTR"].dp = 10.;
// atom["HCTR"].dp = 10.;
// atom["HHIS"].dp = 10.;
//Move::Isobaric iso(mcp,pot,spc);
Move::TranslateRotate gmv(mcp,pot,spc);
Move::AtomicTranslation mv(mcp, pot, spc);
Move::AtomicTranslation mv2(mcp, pot, spc, "ion");
Move::SwapMove tit(mcp,pot,spc);
Move::CrankShaft crank(mcp, pot, spc);
Move::Pivot pivot(mcp, pot, spc);
Move::ParallelTempering temper(mcp,pot,spc,mpi);
Move::Reptation rep(mcp, pot, spc);
Analysis::RadialDistribution<float,int> rdf(0.25);
#ifdef SLIT
Analysis::LineDistribution<float,int> surfdist(0.25), surfmapall(0.25);
//std::map< string , Analysis::LineDistribution<float,int> > surfmap, surfmapall;
std::map< int , Analysis::LineDistribution<float,int> > surfmap_res;
typedef Analysis::Table2D<double, Average<double> > Ttable;
std::map<string , Ttable> dst_map;
#endif
Analysis::ChargeMultipole mpol;
Analysis::PolymerShape shape;
spc.load(textio::prefix+"state");
sys.init( Energy::systemEnergy(spc,pot,spc.p) );
mpi.cout << atom.info() << spc.info() << pot.info() << tit.info()
<< textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int k,i=rand() % 6;
switch (i) {
case 0: // translate and rotate molecules
k=pol.size()+salt.size();
while (k-->0) {
int s=rand()%2;
if (s==1) {
gmv.setGroup( pol.at( rand() % pol.size() ) );
sys+=gmv.move();
}
else {
mv2.setGroup(salt); // translate salt particles
if (salt.size()>0)
sys+=mv2.move( rand() % salt.size() );
}
}
#ifdef SLIT
for (auto &g : pol) {
//surfmap[g.name]( gouy->dist2surf(g.cm) )++;
surfdist( gouy->dist2surf(g.cm) )++; // polymer mass center to GC surface histogram
for (int i=g.front(); i<=g.back(); i++) {
surfmap_res[i]( gouy->dist2surf( spc.p[i] ) )++; // monomer to GC surface histogram
surfmapall( gouy->dist2surf( spc.p.at(i) ) )++;
}
}
#endif
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) )++; // sample polymer-polymer rdf
break;
case 1:
mv.setGroup(allpol);
sys+=mv.move( allpol.size() ); // translate monomers
for (auto &g : pol) {
g.setMassCenter(spc);
shape.sample(g,spc);
}
break;
case 2: // titration move
sys+=tit.move();
mpol.sample(pol,spc);
break;
case 3: // crankshaft move
k=pol.size();
while (k-->0) {
crank.setGroup( pol[ rand() % pol.size() ] );
sys+=crank.move();
}
for (auto &g : pol) {
g.setMassCenter(spc);
shape.sample(g,spc);
}
break;
case 4: // pivot move
k=pol.size();
while (k-->0) {
pivot.setGroup( pol[ rand() % pol.size() ] );
sys+=pivot.move();
}
for (auto &g : pol) {
g.setMassCenter(spc);
shape.sample(g,spc);
}
break;
case 5: // reptation move
k=pol.size();
while (k-->0) {
rep.setGroup( pol[ rand() % pol.size() ] );
sys+=rep.move();
}
for (auto &g : pol) {
g.setMassCenter(spc);
shape.sample(g,spc);
}
break;
//case 5: // volume move
//sys+=iso.move();
// break;
}
if ( slp_global.runtest(0.00001) ) {
xtc.setbox( nonbonded->geometry.len );
xtc.save(textio::prefix+"traj.xtc", spc);
}
//if ( slp_global.runtest(0.1) )
//(*mfc).sample(spc.p, )
#ifdef SLIT
if ( slp_global.runtest(0.1) ) {
for (auto &g : pol) {
double d = gouy->dist2surf(g.cm);
dst_map["Q"]( d )+=g.charge(spc.p);
Point p=shape.vectorgyrationRadiusSquared(g, spc);
dst_map["Rg2"]( d )+=p.x()+p.y()+p.z();
dst_map["Rg2x"]( d )+=p.x();
dst_map["Rg2z"]( d )+=p.z();
dst_map["Ree2"]( d )+=spc.geo->sqdist( spc.p[g.front()], spc.p[g.back()] );
//dst_map["<Energy>"]( d )+=sys.current();
for (int i=g.front(); i<=g.back(); i++){
ostringstream o;
o << "qres" << i ;
dst_map[o.str()]( d )+=spc.p[i].charge;
}
}
}
#endif
} // end of micro loop
temper.setCurrentEnergy( sys.current() );
sys+=temper.move();
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) );
mpi.cout << loop.timing();
cout << loop.timing();
rdf.save(textio::prefix+"rdf_p2p.dat");
#ifdef SLIT
surfdist.save(textio::prefix+"surfdist.dat");
surfmapall.save(textio::prefix+"surfall.dat");
dst_map["Q"].save(textio::prefix+"netq.dat");
//dst_map["<Energy>"].save(textio::prefix+"aveenergy.dat");
for (auto &g : pol){ //Saving averages
//surfmap[g.name].save(textio::prefix+g.name+"surfdist.dat");
std::ofstream f(textio::prefix+"res-surfdist.dat");
std::ofstream f1(textio::prefix+"Rg-comp.dat");
std::ofstream f2(textio::prefix+"qres.dat");
f.precision(7);
f1.precision(7);
f2.precision(7);
if (f && f1 && f2) {
//f << "#g(z) of each residue from 1 to " << g.size() << endl;
for (double d=0; d<=nonbonded->geometry.len.z(); d+=0.25){
f1 << d;
if (dst_map["Rg2"](d).cnt > 0) f1 << "\t" << dst_map["Rg2"](d); //If counter is empty, then it prints shit lot of warning
else f1 << "\t0";
if (dst_map["Rg2x"](d).cnt > 0)f1 << "\t" << dst_map["Rg2x"](d);
else f1 << "\t0";
if (dst_map["Rg2z"](d).cnt > 0) f1 << "\t" << dst_map["Rg2z"](d);
else f1 << "\t0";
if (dst_map["Ree2"](d).cnt > 0) f1 << "\t" << dst_map["Ree2"](d);
else f1 << "\t0";
f1 << endl;
f << d;
f2 << d;
for (int i=g.front(); i<=g.back(); i++){
f << "\t" << surfmap_res[i](d);
ostringstream o;
o << "qres" << i ;
if (dst_map[o.str()]( d ).cnt > 0 ) f2 << "\t" << dst_map[o.str()]( d );
else f2 << "\t0";
}
f << endl;
f2 << endl;
}
}
}
#endif
pqr.save(textio::prefix+"confout.pqr", spc.p);
aam.save(textio::prefix+"confout.aam", spc.p);
mcp.save(textio::prefix+"mdout.mdp");
spc.save(textio::prefix+"state");
} // end of macro loop
mpi.cout << loop.info() << sys.info() << gmv.info() << mv.info() << mv2.info()
<< crank.info() << pivot.info() << rep.info() << temper.info()
<< tit.info() << mpol.info() << shape.info() << spc.info();
tit.applycharges(spc.p);
pqr.save(textio::prefix+"conf_aveq.pqr", spc.p);
aam.save(textio::prefix+"conf_aveq.aam", spc.p);
}
int main(int argc, char** argv) {
#ifdef TEMPER
#define cout mpi.cout
Faunus::MPI::MPIController mpi;
#endif
cout << textio::splash();
InputMap mcp(textio::prefix+"gouychapman.input");
MCLoop loop(mcp); // class for handling mc loops
FormatPQR pqr; // PQR structure file I/O
FormatAAM aam; // AAM structure file I/O
FormatXTC xtc(1000); // XTC gromacs trajectory format for only cuboid geomtries
EnergyDrift sys; // class for tracking system energy drifts
Tspace spc(mcp);
auto pot = Energy::Nonbonded<Tspace, Tpairpot>(mcp) +
Energy::ExternalPotential<Tspace,Potential::GouyChapman<> >(mcp);
pot.second.setSurfPositionZ( &spc.geo.len_half.z() );
pot.setSpace(spc);
// Add rigid molecules
vector<GroupMolecular> pol( mcp.get("polymer_N",0));
string polyfile = mcp.get<string>("polymer_file", "");
for (auto &g : pol) { // load molecules
aam.load(polyfile);
Geometry::FindSpace f;
f.find(*spc.geo, spc.p, aam.p); // find empty spot in particle vector
g = spc.insert( aam.p ); // insert into space
g.name="Molecule";
spc.enroll(g);
}
Move::TranslateRotate<Tspace> gmv(mcp,pot,spc);
#ifdef TEMPER
Move::ParallelTempering<Tspace> temper(mcp,pot,spc,mpi);
#endif
Analysis::RadialDistribution<float,int> rdf(0.25);
Analysis::LineDistribution<float,int> surfdist(0.25);
spc.load(textio::prefix+"state");
pqr.save(textio::prefix+"initial.pqr", spc.p);
sys.init( Energy::systemEnergy(spc,pot,spc.p) );
cout << atom.info() << spc.info() << pot.info() << textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int k,i= slump.rand() % 1;
switch (i) {
case 0: // translate and rotate molecules
k=pol.size();
while (k-->0) {
gmv.setGroup( pol[ slump.rand() % pol.size() ] );
sys+=gmv.move();
}
for (auto &g : pol)
surfdist( gouy->dist2surf(g.cm) )++; // molecule mass center to GC surface histogram
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) )++; // molecule-molecule rdf
break;
}
if ( slump.runtest(0.0001) ) {
xtc.setbox( spc.geo.len );
xtc.save(textio::prefix+"traj.xtc", spc); // gromacs xtc file output
}
} // end of micro loop
#ifdef TEMPER
temper.setCurrentEnergy( sys.current() );
sys+=temper.move();
#endif
sys.checkDrift( Energy::systemEnergy(spc,pot,spc.p) );
cout << loop.timing();
rdf.save(textio::prefix+"rdf_p2p.dat");
surfdist.save(textio::prefix+"surfdist.dat");
pqr.save(textio::prefix+"confout.pqr", spc.p);
spc.save(textio::prefix+"state");
} // end of macro loop
cout << loop.info() << pot.first.info() << sys.info() << gmv.info();
#ifdef TEMPER
cout << temper.info();
#endif
}
int main() {
Group g(100,1);
g.resize(0);
cout << "size = " << g.size() << endl;
cout << "range = " << g.front() << " " << g.back() << endl;
cout << "empty bool = " << g.empty() << endl;
for (auto i=g.begin(); i!=g.end(); i++)
cout << *i << endl;
cout << textio::splash();
atom.includefile("atomlist.inp"); // load atom properties
InputMap mcp("bulk.inp");
MCLoop loop(mcp); // class for handling mc loops
FormatPQR pqr; // PQR structure file I/O
EnergyDrift sys; // class for tracking system energy drifts
Energy::Hamiltonian pot;
auto nonbonded = pot.create( Energy::Nonbonded<Tpairpot,Tgeometry>(mcp) );
Space spc( pot.getGeometry() );
// Handle particles
GroupAtomic salt(spc, mcp);
salt.name="Salt";
spc.load("space.state", Space::RESIZE);
Move::GrandCanonicalSalt gc(mcp,pot,spc,salt);
Move::AtomicTranslation mv(mcp, pot, spc); // Particle move class
mv.setGroup(salt);
// Widom particle insertion
Analysis::RadialDistribution<float,unsigned int> rdf(0.2);
rdf.maxdist = 50.;
particle a;
Analysis::Widom widom(spc, pot);
a = atom["Cl"];
widom.addGhost( spc);
widom.addGhost( a );
#define UTOTAL \
+ pot.g_internal(spc.p, salt) + pot.g_external(spc.p, salt)\
+ pot.external()
sys.init( UTOTAL );
cout << atom.info() << spc.info() << pot.info() << mv.info()
<< textio::header("MC Simulation Begins!");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
sys+=mv.move( salt.size() );
sys+=gc.move( salt.size()/2 );
if (slp_global.randOne()>0.9) {
widom.sample();
rdf.sample(spc,salt,atom["Na"].id, atom["Cl"].id);
}
}
sys.checkDrift( UTOTAL );
cout << loop.timing();
}
pqr.save("confout.pqr", spc.p);
spc.save("space.state");
rdf.save("rdf.dat");
cout << sys.info() << loop.info() << mv.info() << gc.info() << widom.info();
}
int main() {
cout << textio::splash(); // show faunus banner and credits
InputMap mcp("sc-npt.input"); // open user input file
MCLoop loop(mcp); // class for handling mc loops
FormatPQR pqr; // PQR structure file I/O
EnergyDrift sys; // class for tracking system energy drifts
// Energy functions and space
Tspace spc(mcp);
auto pot = Energy::NonbondedVector<Tspace,Tpairpot>(mcp)
+ Energy::ExternalPressure<Tspace>(mcp);
// Markov moves and analysis
Move::Isobaric<Tspace> iso(mcp,pot,spc);
Move::AtomicTranslation<Tspace> mv(mcp, pot, spc);
Move::AtomicRotation<Tspace> rot(mcp, pot, spc);
Analysis::RadialDistribution<> rdf(0.2);
// Add cigars
Group cigars;
cigars.addParticles(spc, mcp);
cigars.name="cigars";
for (auto i : cigars) {
spc.p[i].halfl = 2.5;
spc.p[i].dir.ranunit(slp_global);
spc.trial[i]=spc.p[i];
}
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!");
std::ofstream m("snapshot");
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int i=slp_global.rand() % 3;
switch (i) {
case 0:
mv.setGroup(cigars);
sys+=mv.move( cigars.size() ); // translate cigars
break;
case 1:
rot.setGroup(cigars);
sys+=rot.move( cigars.size() ); // translate cigars
break;
case 2:
sys+=iso.move(); // isobaric volume move
break;
}
// movie
if (slp_global()<0.001)
{
m << spc.p.size() << "\n"
<< "sweep " << loop.count() << "; box "
<< spc.geo.len.x() << " "
<< spc.geo.len.y() << " "
<< spc.geo.len.z() << "\n";
for (auto &i : spc.p) {
m << i.x() << " " << i.y() << " " << i.z() << " "
<< i.dir.x() << " " << i.dir.y() << " " << i.dir.z() << " "
<< " 0 0 0 0\n";
}
}
} // end of micro loop
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");
pqr.save("confout.pqr", spc.p);
spc.save("state");
// print information
cout << loop.info() << sys.info() << mv.info() << rot.info() << iso.info();
}
int main() {
InputMap mcp("water2.input");//read input file
slp_global.seed(mcp.get<int>("seed", -7));
// Energy functions and space
auto pot = Energy::NonbondedVector<Tspace,Tpairpot>(mcp)
+ Energy::ExternalPressure<Tspace>(mcp);
Tspace spc(mcp);
// Load and add polymer to Space
auto N = mcp.get<int>("mol_N",1);
auto file = mcp.get<string>("mol_file");
vector<Group> water(N);
Tspace::ParticleVector v; // temporary, empty particle vector
FormatAAM::load(file,v); // load AAM structure into v
for (auto &i : water) {
Geometry::FindSpace f;
f.allowMatterOverlap=true;
f.find(spc.geo,spc.p,v);// find empty spot in particle vector
i = spc.insert(v); // Insert into Space
i.name="h2o";
spc.enroll(i);
}
// Markov moves and analysis
Move::PolarizeMove<TranslateRotate<Tspace> > gmv(mcp,pot,spc);
//Move::TranslateRotate<Tspace> gmv(mcp,pot,spc);
Move::Isobaric<Tspace> iso(mcp,pot,spc);
Analysis::RadialDistribution<> rdfOO(0.05);
Analysis::RadialDistribution<> rdfOH(0.05);
Analysis::RadialDistribution<> rdfHH(0.05);
spc.load("state"); // load old config. from disk (if any)
Analysis::DipoleAnalysis dian(spc,mcp);
dian.load(mcp.get<string>("dipole_data_ext", ""));
FormatPQR::save("initial.pqr", spc.p);
EnergyDrift sys; // class for tracking system energy drifts
sys.init( Energy::systemEnergy(spc,pot,spc.p) ); // store total energy
cout << atom.info() + spc.info() + pot.info() + textio::header("MC Simulation Begins!");
MCLoop loop(mcp); // class for handling mc loops
while ( loop.macroCnt() ) { // Markov chain
while ( loop.microCnt() ) {
int i=slp_global.rand() % 2;
int j,k=water.size();
Group g;
switch (i) {
case 0:
while (k-->0) {
j=slp_global.rand() % (water.size());
gmv.setGroup(water[j]);
sys+=gmv.move(); // translate/rotate polymers
}
break;
case 1:
sys+=iso.move();
break;
}
dian.sampleDP(spc);
// sample oxygen-oxygen rdf
if (slp_global()>0.5) {
dian.sampleMuCorrelationAndKirkwood(spc);
auto idO = atom["OW"].id;
auto idH = atom["HW"].id;
rdfOO.sample(spc,idO,idO);
rdfOH.sample(spc,idO,idH);
rdfHH.sample(spc,idH,idH);
}
} // end of micro loop
//rdfOO.save("rdfOO.dat"+std::to_string(loop.count()));
//rdfOH.save("rdfOH.dat"+std::to_string(loop.count()));
//rdfHH.save("rdfHH.dat"+std::to_string(loop.count()));
//dian.save(std::to_string(loop.count()));
sys.checkDrift(Energy::systemEnergy(spc,pot,spc.p)); // energy drift?
cout << loop.timing();
} // end of macro loop
// save to disk
spc.save("state");
rdfOO.save("rdfOO.dat");
rdfOH.save("rdfOH.dat");
rdfHH.save("rdfHH.dat");
spc.save("state");
dian.save();
FormatPQR::save("confout.pqr", spc.p, spc.geo.len);
// print information
cout << loop.info() + sys.info() + gmv.info() + iso.info() + dian.info();
}
