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(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) {
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) {
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();
}