int main(int, char **) {
FILE *o = fopen("paper/figs/constrained-water.dat", "w");
Functional f = OfEffectivePotential(SaftFluidSlow(water_prop.lengthscale,
water_prop.epsilonAB, water_prop.kappaAB,
water_prop.epsilon_dispersion,
water_prop.lambda_dispersion, water_prop.length_scaling, 0));
double mu_satp = find_chemical_potential(f, water_prop.kT,
water_prop.liquid_density);
Lattice lat(Cartesian(width,0,0), Cartesian(0,width,0), Cartesian(0,0,zmax));
GridDescription gd(lat, 0.1);
Grid potential(gd);
Grid constraint(gd);
constraint.Set(notinwall);
f = constrain(constraint,
OfEffectivePotential(SaftFluidSlow(water_prop.lengthscale,
water_prop.epsilonAB, water_prop.kappaAB,
water_prop.epsilon_dispersion,
water_prop.lambda_dispersion, water_prop.length_scaling, mu_satp)));
Minimizer min = Precision(0, PreconditionedConjugateGradient(f, gd, water_prop.kT, &potential,
QuadraticLineMinimizer));
potential = water_prop.liquid_density*constraint
+ water_prop.vapor_density*VectorXd::Ones(gd.NxNyNz);
//potential = water_prop.liquid_density*VectorXd::Ones(gd.NxNyNz);
potential = -water_prop.kT*potential.cwise().log();
const int numiters = 50;
for (int i=0;i<numiters && min.improve_energy(true);i++) {
fflush(stdout);
Grid density(gd, EffectivePotentialToDensity()(water_prop.kT, gd, potential));
density.epsNative1d("paper/figs/1d-constrained-plot.eps",
Cartesian(0,0,0), Cartesian(0,0,zmax),
water_prop.liquid_density, 1, "Y axis: , x axis: ");
}
min.print_info();
double energy = min.energy()/width/width;
printf("Energy is %.15g\n", energy);
double N = 0;
{
Grid density(gd, EffectivePotentialToDensity()(water_prop.kT, gd, potential));
for (int i=0;i<gd.NxNyNz;i++) N += density[i]*gd.dvolume;
}
N = N/width/width;
printf("N is %.15g\n", N);
Grid density(gd, EffectivePotentialToDensity()(water_prop.kT, gd, potential));
density.epsNative1d("paper/figs/1d-constrained-plot.eps", Cartesian(0,0,0), Cartesian(0,0,zmax), water_prop.liquid_density, 1, "Y axis: , x axis: ");
//potential.epsNative1d("hard-wall-potential.eps", Cartesian(0,0,0), Cartesian(0,0,zmax), 1, 1);
fclose(o);
}
int main(int argc, char *argv[]) {
if (argc > 1) {
if (sscanf(argv[1], "%lg", &diameter) != 1) {
printf("Got bad argument: %s\n", argv[1]);
return 1;
}
diameter *= nm;
using_default_diameter = false;
printf("Diameter is %g bohr\n", diameter);
}
const double ptransition =(3.0*M_PI-4.0)*(diameter/2.0)/2.0;
const double dmax = ptransition + 0.6*nm;
double zmax = 2*diameter+dmax+2*nm;
double ymax = 2*diameter+dmax+2*nm;
char *datname = new char[1024];
snprintf(datname, 1024, "papers/water-saft/figs/four-rods-in-water-%04.1fnm.dat", diameter/nm);
FILE *o = fopen(datname, "w");
delete[] datname;
Functional f = OfEffectivePotential(WaterSaft(new_water_prop.lengthscale,
new_water_prop.epsilonAB, new_water_prop.kappaAB,
new_water_prop.epsilon_dispersion,
new_water_prop.lambda_dispersion,
new_water_prop.length_scaling, 0));
double n_1atm = pressure_to_density(f, new_water_prop.kT, atmospheric_pressure,
0.001, 0.01);
double mu_satp = find_chemical_potential(f, new_water_prop.kT, n_1atm);
f = OfEffectivePotential(WaterSaft(new_water_prop.lengthscale,
new_water_prop.epsilonAB, new_water_prop.kappaAB,
new_water_prop.epsilon_dispersion,
new_water_prop.lambda_dispersion,
new_water_prop.length_scaling, mu_satp));
const double EperVolume = f(new_water_prop.kT, -new_water_prop.kT*log(n_1atm));
const double EperCell = EperVolume*(zmax*ymax - 4*0.25*M_PI*diameter*diameter)*width;
//Functional X = Xassociation(new_water_prop.lengthscale, new_water_prop.epsilonAB,
// new_water_prop.kappaAB, new_water_prop.epsilon_dispersion,
// new_water_prop.lambda_dispersion,
// new_water_prop.length_scaling);
Functional S = OfEffectivePotential(EntropySaftFluid2(new_water_prop.lengthscale,
new_water_prop.epsilonAB,
new_water_prop.kappaAB,
new_water_prop.epsilon_dispersion,
new_water_prop.lambda_dispersion,
new_water_prop.length_scaling));
//dmax, dstep already in bohrs (so it doesn't need to be converted from nm)
double dstep = 0.25*nm;
for (distance=0.0*nm; distance<=dmax; distance += dstep) {
if ((distance >= ptransition - 0.5*nm) && (distance <= ptransition + 0.05*nm)) {
if (distance >= ptransition - 0.25*nm) {
dstep = 0.03*nm;
} else {
dstep = 0.08*nm;
}
} else {
dstep = 0.25*nm;
}
Lattice lat(Cartesian(width,0,0), Cartesian(0,ymax,0), Cartesian(0,0,zmax));
GridDescription gd(lat, 0.2);
printf("Grid is %d x %d x %d\n", gd.Nx, gd.Ny, gd.Nz);
Grid potential(gd);
Grid constraint(gd);
constraint.Set(notinwall);
f = OfEffectivePotential(WaterSaft(new_water_prop.lengthscale,
new_water_prop.epsilonAB, new_water_prop.kappaAB,
new_water_prop.epsilon_dispersion,
new_water_prop.lambda_dispersion,
new_water_prop.length_scaling, mu_satp));
f = constrain(constraint, f);
printf("Diameter is %g bohr (%g nm)\n", diameter, diameter/nm);
printf("Distance between rods = %g bohr (%g nm)\n", distance, distance/nm);
potential = new_water_prop.liquid_density*constraint
+ 400*new_water_prop.vapor_density*VectorXd::Ones(gd.NxNyNz);
//potential = new_water_prop.liquid_density*VectorXd::Ones(gd.NxNyNz);
potential = -new_water_prop.kT*potential.cwise().log();
const double surface_tension = 5e-5; // crude guess from memory...
const double surfprecision = 1e-5*(4*M_PI*diameter)*width*surface_tension; // five digits accuracy
const double bulkprecision = 1e-12*fabs(EperCell); // but there's a limit on our precision for small rods
const double precision = bulkprecision + surfprecision;
printf("Precision limit from surface tension is to %g based on %g and %g\n",
precision, surfprecision, bulkprecision);
Minimizer min = Precision(precision, PreconditionedConjugateGradient(f, gd, new_water_prop.kT,
&potential,
QuadraticLineMinimizer));
const int numiters = 200;
for (int i=0;i<numiters && min.improve_energy(false);i++) {
fflush(stdout);
// {
// double peak = peak_memory()/1024.0/1024;
// double current = current_memory()/1024.0/1024;
// printf("Peak memory use is %g M (current is %g M)\n", peak, current);
// }
}
Grid potential2(gd);
Grid constraint2(gd);
constraint2.Set(notinmiddle);
potential2 = new_water_prop.liquid_density*(constraint2.cwise()*constraint)
+ 400*new_water_prop.vapor_density*VectorXd::Ones(gd.NxNyNz);
potential2 = -new_water_prop.kT*potential2.cwise().log();
Minimizer min2 = Precision(1e-12, PreconditionedConjugateGradient(f, gd, new_water_prop.kT,
&potential2,
QuadraticLineMinimizer));
for (int i=0;i<numiters && min2.improve_energy(false);i++) {
fflush(stdout);
// {
// double peak = peak_memory()/1024.0/1024;
// double current = current_memory()/1024.0/1024;
// printf("Peak memory use is %g M (current is %g M)\n", peak, current);
// }
}
char *plotnameslice = new char[1024];
snprintf(plotnameslice, 1024, "papers/water-saft/figs/four-rods-%04.1f-%04.2f.dat", diameter/nm, distance/nm);
printf("The bulk energy per cell should be %g\n", EperCell);
double energy;
if (min.energy() < min2.energy()) {
energy = (min.energy() - EperCell)/width;
Grid density(gd, EffectivePotentialToDensity()(new_water_prop.kT, gd, potential));
printf("Using liquid in middle initially.\n");
plot_grids_yz_directions(plotnameslice, density);
{
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
}
} else {
energy = (min2.energy() - EperCell)/width;
Grid density(gd, EffectivePotentialToDensity()(new_water_prop.kT, gd, potential2));
printf("Using vapor in middle initially.\n");
plot_grids_yz_directions(plotnameslice, density);
{
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
}
}
printf("Liquid energy is %.15g. Vapor energy is %.15g\n", min.energy(), min2.energy());
fprintf(o, "%g\t%.15g\n", distance/nm, energy);
//Grid entropy(gd, S(new_water_prop.kT, potential));
//Grid Xassoc(gd, X(new_water_prop.kT, density));
//plot_grids_y_direction(plotnameslice, density, energy_density, entropy, Xassoc);
//Grid energy_density(gd, f(new_water_prop.kT, gd, potential));
delete[] plotnameslice;
}
fclose(o);
{
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
}
}
int main(int argc, char *argv[]) {
clock_t start_time = clock();
if (argc > 1) {
if (sscanf(argv[1], "%lg", &diameter) != 1) {
printf("Got bad argument: %s\n", argv[1]);
return 1;
}
diameter *= nm;
using_default_diameter = false;
}
printf("Diameter is %g bohr = %g nm\n", diameter, diameter/nm);
const double padding = 1*nm;
xmax = ymax = zmax = diameter + 2*padding;
char *datname = (char *)malloc(1024);
sprintf(datname, "papers/hughes-saft/figs/sphere-%04.2fnm-energy.dat", diameter/nm);
Functional f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, 0));
double n_1atm = pressure_to_density(f, hughes_water_prop.kT, atmospheric_pressure,
0.001, 0.01);
double mu_satp = find_chemical_potential(f, hughes_water_prop.kT, n_1atm);
f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu_satp));
Functional S = OfEffectivePotential(EntropySaftFluid2(new_water_prop.lengthscale,
new_water_prop.epsilonAB,
new_water_prop.kappaAB,
new_water_prop.epsilon_dispersion,
new_water_prop.lambda_dispersion,
new_water_prop.length_scaling));
const double EperVolume = f(hughes_water_prop.kT, -hughes_water_prop.kT*log(n_1atm));
const double EperNumber = EperVolume/n_1atm;
const double SperNumber = S(hughes_water_prop.kT, -hughes_water_prop.kT*log(n_1atm))/n_1atm;
const double EperCell = EperVolume*(zmax*ymax*xmax - (M_PI/6)*diameter*diameter*diameter);
//for (diameter=0*nm; diameter<3.0*nm; diameter+= .1*nm) {
Lattice lat(Cartesian(xmax,0,0), Cartesian(0,ymax,0), Cartesian(0,0,zmax));
GridDescription gd(lat, 0.2);
Grid potential(gd);
Grid constraint(gd);
constraint.Set(notinwall);
f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu_satp));
f = constrain(constraint, f);
//constraint.epsNativeSlice("papers/hughes-saft/figs/sphere-constraint.eps",
// Cartesian(0,ymax,0), Cartesian(0,0,zmax),
// Cartesian(0,ymax/2,zmax/2));
//printf("Constraint has become a graph!\n");
potential = hughes_water_prop.liquid_density*constraint
+ 100*hughes_water_prop.vapor_density*VectorXd::Ones(gd.NxNyNz);
//potential = hughes_water_prop.liquid_density*VectorXd::Ones(gd.NxNyNz);
potential = -hughes_water_prop.kT*potential.cwise().log();
double energy;
{
const double surface_tension = 5e-5; // crude guess from memory...
const double surfprecision = 1e-4*M_PI*diameter*diameter*surface_tension; // four digits precision
const double bulkprecision = 1e-12*fabs(EperCell); // but there's a limit on our precision for small spheres
const double precision = bulkprecision + surfprecision;
Minimizer min = Precision(precision,
PreconditionedConjugateGradient(f, gd, hughes_water_prop.kT,
&potential,
QuadraticLineMinimizer));
printf("\nDiameter of sphere = %g bohr (%g nm)\n", diameter, diameter/nm);
const int numiters = 200;
for (int i=0;i<numiters && min.improve_energy(true);i++) {
//fflush(stdout);
//Grid density(gd, EffectivePotentialToDensity()(hughes_water_prop.kT, gd, potential));
//density.epsNativeSlice("papers/hughes-saft/figs/sphere.eps",
// Cartesian(0,ymax,0), Cartesian(0,0,zmax),
// Cartesian(0,ymax/2,zmax/2));
//sleep(3);
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
}
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
energy = min.energy();
printf("Total energy is %.15g\n", energy);
// Here we free the minimizer with its associated data structures.
}
{
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
}
double entropy = S.integral(hughes_water_prop.kT, potential);
Grid density(gd, EffectivePotentialToDensity()(hughes_water_prop.kT, gd, potential));
printf("Number of water molecules is %g\n", density.integrate());
printf("The bulk energy per cell should be %g\n", EperCell);
printf("The bulk energy based on number should be %g\n", EperNumber*density.integrate());
printf("The bulk entropy is %g/N\n", SperNumber);
Functional otherS = EntropySaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB,
hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling);
printf("The bulk entropy (haskell) = %g/N\n", otherS(hughes_water_prop.kT, n_1atm)/n_1atm);
//printf("My entropy is %g when I would expect %g\n", entropy, entropy - SperNumber*density.integrate());
double hentropy = otherS.integral(hughes_water_prop.kT, density);
otherS.print_summary(" ", hentropy, "total entropy");
printf("My haskell entropy is %g, when I would expect = %g, difference is %g\n", hentropy,
otherS(hughes_water_prop.kT, n_1atm)*density.integrate()/n_1atm,
hentropy - otherS(hughes_water_prop.kT, n_1atm)*density.integrate()/n_1atm);
FILE *o = fopen(datname, "w");
//fprintf(o, "%g\t%.15g\n", diameter/nm, energy - EperCell);
fprintf(o, "%g\t%.15g\t%.15g\t%.15g\t%.15g\n", diameter/nm, energy - EperNumber*density.integrate(), energy - EperCell,
hughes_water_prop.kT*(entropy - SperNumber*density.integrate()),
hughes_water_prop.kT*(hentropy - otherS(hughes_water_prop.kT, n_1atm)*density.integrate()/n_1atm));
fclose(o);
char *plotname = (char *)malloc(1024);
sprintf(plotname, "papers/hughes-saft/figs/sphere-%04.2f.dat", diameter/nm);
plot_grids_y_direction(plotname, density);
free(plotname);
//density.epsNativeSlice("papers/hughes-saft/figs/sphere.eps",
// Cartesian(0,ymax,0), Cartesian(0,0,zmax),
// Cartesian(0,ymax/2,zmax/2));
double peak = peak_memory()/1024.0/1024;
printf("Peak memory use is %g M\n", peak);
double oldN = density.integrate();
density = n_1atm*VectorXd::Ones(gd.NxNyNz);;
double hentropyb = otherS.integral(hughes_water_prop.kT, density);
printf("bulklike thingy has %g molecules\n", density.integrate());
otherS.print_summary(" ", hentropyb, "bulk-like entropy");
printf("entropy difference is %g\n", hentropy - hentropyb*oldN/density.integrate());
// }
clock_t end_time = clock();
double seconds = (end_time - start_time)/double(CLOCKS_PER_SEC);
double hours = seconds/60/60;
printf("Entire calculation took %.0f hours %.0f minutes\n", hours, 60*(hours-floor(hours)));
}
int main(int argc, char *argv[]) {
if (argc == 5) {
if (sscanf(argv[1], "%lg", &xmax) != 1) {
printf("Got bad x argument: %s\n", argv[1]);
return 1;
}
if (sscanf(argv[2], "%lg", &ymax) != 1) {
printf("Got bad y argument: %s\n", argv[2]);
return 1;
}
if (sscanf(argv[3], "%lg", &zmax) != 1) {
printf("Got bad z argument: %s\n", argv[3]);
return 1;
}
if (sscanf(argv[4], "%lg", &N) != 1) {
printf("Got bad N argument: %s\n", argv[4]);
return 1;
}
using_default_box = false;
printf("Box is %g x %g x %g hard sphere diameters, and it holds %g of them\n", xmax, ymax, zmax, N);
}
char *datname = (char *)malloc(1024);
sprintf(datname, "papers/contact/figs/box-%02.0f,%02.0f,%02.0f-%02.0f-energy.dat", xmax, ymax, zmax, N);
FILE *o = fopen(datname, "w");
const double myvolume = (xmax+2)*(ymax+2)*(zmax+2);
const double meandensity = N/myvolume;
Functional f = OfEffectivePotential(HS + IdealGas());
double mu = find_chemical_potential(f, 1, meandensity);
f = OfEffectivePotential(HS + IdealGas()
+ ChemicalPotential(mu));
Lattice lat(Cartesian(xmax+3,0,0), Cartesian(0,ymax+3,0), Cartesian(0,0,zmax+3));
GridDescription gd(lat, 0.05);
Grid potential(gd);
Grid constraint(gd);
constraint.Set(notinwall);
took("Setting the constraint");
printf("xmax = %g\nymax = %g\nzmax = %g\nmeandensity=%g\n", xmax, ymax, zmax, meandensity);
f = constrain(constraint, f);
constraint.epsNativeSlice("papers/contact/figs/box-constraint.eps",
Cartesian(0,ymax+4,0), Cartesian(0,0,zmax+4),
Cartesian(0,-ymax/2-2,-zmax/2-2));
printf("Constraint has become a graph!\n");
potential = meandensity*constraint + 1e-4*meandensity*VectorXd::Ones(gd.NxNyNz);
potential = -potential.cwise().log();
Minimizer min = Precision(1e-6,
PreconditionedConjugateGradient(f, gd, 1,
&potential,
QuadraticLineMinimizer));
double mumax = mu, mumin = mu, dmu = 4.0/N;
double Nnow = N_from_mu(&min, &potential, constraint, mu);
const double fraccuracy = 1e-3;
if (fabs(Nnow/N - 1) > fraccuracy) {
if (Nnow > N) {
while (Nnow > N) {
mumin = mumax;
mumax += dmu;
dmu *= 2;
Nnow = N_from_mu(&min, &potential, constraint, mumax);
// Grid density(gd, EffectivePotentialToDensity()(1, gd, potential));
// density = EffectivePotentialToDensity()(1, gd, potential);
// density.epsNativeSlice("papers/contact/figs/box.eps",
// Cartesian(0,ymax+2,0), Cartesian(0,0,zmax+2),
// Cartesian(0,-ymax/2-1,-zmax/2-1));
// density.epsNativeSlice("papers/contact/figs/box-diagonal.eps",
// Cartesian(xmax+2,0,zmax+2), Cartesian(0,ymax+2,0),
// Cartesian(-xmax/2-1,-ymax/2-1,-zmax/2-1));
printf("mumax %g gives N %g\n", mumax, Nnow);
took("Finding N from mu");
}
printf("mu is between %g and %g\n", mumin, mumax);
} else {
while (Nnow < N) {
mumax = mumin;
if (mumin > dmu) {
mumin -= dmu;
dmu *= 2;
} else if (mumin > 0) {
mumin = -mumin;
} else {
mumin *= 2;
}
Nnow = N_from_mu(&min, &potential, constraint, mumin);
// density = EffectivePotentialToDensity()(1, gd, potential);
// density.epsNativeSlice("papers/contact/figs/box.eps",
// Cartesian(0,ymax+2,0), Cartesian(0,0,zmax+2),
// Cartesian(0,-ymax/2-1,-zmax/2-1));
// density.epsNativeSlice("papers/contact/figs/box-diagonal.eps",
// Cartesian(xmax+2,0,zmax+2), Cartesian(0,ymax+2,0),
// Cartesian(-xmax/2-1,-ymax/2-1,-zmax/2-1));
printf("mumin %g gives N %g\n", mumin, Nnow);
took("Finding N from mu");
}
printf("mu is between %g and %g\n", mumin, mumax);
}
while (fabs(N/Nnow-1) > fraccuracy) {
mu = 0.5*(mumin + mumax);
Nnow = N_from_mu(&min, &potential, constraint, mu);
// density = EffectivePotentialToDensity()(1, gd, potential);
// density.epsNativeSlice("papers/contact/figs/box.eps",
// Cartesian(0,ymax+2,0), Cartesian(0,0,zmax+2),
// Cartesian(0,-ymax/2-1,-zmax/2-1));
// density.epsNativeSlice("papers/contact/figs/box-diagonal.eps",
// Cartesian(xmax+2,0,zmax+2), Cartesian(0,ymax+2,0),
// Cartesian(-xmax/2-1,-ymax/2-1,-zmax/2-1));
printf("Nnow is %g vs %g with mu %g\n", Nnow, N, mu);
took("Finding N from mu");
if (Nnow > N) {
mumin = mu;
} else {
mumax = mu;
}
}
}
printf("N final is %g (vs %g) with mu = %g\n", Nnow, N, mu);
double energy = min.energy();
printf("Energy is %.15g\n", energy);
Grid density(gd, EffectivePotentialToDensity()(1, gd, potential));
double mean_contact_density = ContactDensitySimplest(1.0).integral(1, density)/myvolume;
fprintf(o, "%g\t%g\t%g\t%.15g\t%.15g\n", xmax, ymax, zmax, energy, mean_contact_density);
Grid energy_density(gd, f(1, gd, potential));
Grid contact_density(gd, ContactDensitySimplest(1.0)(1, gd, density));
Grid n0(gd, ShellConvolve(1)(1, density));
Grid wu_contact_density(gd, FuWuContactDensity(1.0)(1, gd, density));
char *plotname = (char *)malloc(1024);
sprintf(plotname, "papers/contact/figs/box-100c--%02.0f,%02.0f,%02.0f-%02.0f.dat", xmax, ymax, zmax, N);
plot_grids_100_center(plotname, density, energy_density, contact_density);
sprintf(plotname, "papers/contact/figs/box-100s--%02.0f,%02.0f,%02.0f-%02.0f.dat", xmax, ymax, zmax, N);
plot_grids_100_side(plotname, density, energy_density, contact_density);
sprintf(plotname, "papers/contact/figs/box-110c--%02.0f,%02.0f,%02.0f-%02.0f.dat", xmax, ymax, zmax, N);
plot_grids_110(plotname, density, energy_density, contact_density);
sprintf(plotname, "papers/contact/figs/box-x-%02.0f,%02.0f,%02.0f-%02.0f.dat", xmax, ymax, zmax, N);
x_plot(plotname, density, energy_density, contact_density, wu_contact_density);
free(plotname);
density.epsNativeSlice("papers/contact/figs/box.eps",
Cartesian(0,ymax+2,0), Cartesian(0,0,zmax+2),
Cartesian(0,-ymax/2-1,-zmax/2-1));
density.epsNativeSlice("papers/contact/figs/box-diagonal.eps",
Cartesian(xmax+2,0,zmax+2), Cartesian(0,ymax+2,0),
Cartesian(-xmax/2-1,-ymax/2-1,-zmax/2-1));
took("Plotting stuff");
fclose(o);
}
int main(int argc, char *argv[]) {
clock_t start_time = clock();
if (argc == 3) {
if (sscanf(argv[2], "%lg", &temperature) != 1) {
printf("Got bad argument: %s\n", argv[2]);
return 1;
}
temperature *= kB;
bool good_element = false;
for (int i=0; i<numelements; i++) {
if (strcmp(elements[i], argv[1]) == 0) {
sigma = sigmas[i];
epsilon = epsilons[i];
good_element = true;
}
}
if (!good_element) {
printf("Bad element: %s\n", argv[1]);
return 1;
}
} else {
printf("Need element and temperature.\n");
return 1;
}
char *datname = (char *)malloc(1024);
sprintf(datname, "papers/water-saft/figs/hughes-lj-%s-%gK-energy.dat", argv[1], temperature/kB);
Functional f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, 0));
double n_1atm = pressure_to_density(f, temperature, lj_pressure,
0.001, 0.01);
double mu = find_chemical_potential(f, temperature, n_1atm);
f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu));
Functional S = OfEffectivePotential(EntropySaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB,
hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling));
const double EperVolume = f(temperature, -temperature*log(n_1atm));
const double EperNumber = EperVolume/n_1atm;
const double SperNumber = S(temperature, -temperature*log(n_1atm))/n_1atm;
const double EperCell = EperVolume*(zmax*ymax*xmax - (4*M_PI/3)*sigma*sigma*sigma);
Lattice lat(Cartesian(xmax,0,0), Cartesian(0,ymax,0), Cartesian(0,0,zmax));
GridDescription gd(lat, 0.20);
Grid potential(gd);
Grid externalpotential(gd);
externalpotential.Set(externalpotentialfunction);
f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu) + ExternalPotential(externalpotential));
Functional X = WaterX(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu);
Functional HB = HughesHB(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu);
externalpotential.epsNativeSlice("papers/water-saft/figs/hughes-lj-potential.eps",
Cartesian(0,ymax,0), Cartesian(0,0,zmax),
Cartesian(0,ymax/2,zmax/2));
printf("Done outputting hughes-lj-potential.eps\n");
potential = 0*externalpotential - temperature*log(n_1atm)*VectorXd::Ones(gd.NxNyNz); // ???
double energy;
{
const double surface_tension = 5e-5; // crude guess from memory...
const double surfprecision = 1e-4*M_PI*sigma*sigma*surface_tension; // four digits precision
const double bulkprecision = 1e-12*fabs(EperCell); // but there's a limit on our precision
const double precision = (bulkprecision + surfprecision)*1e-6;
Minimizer min = Precision(precision,
PreconditionedConjugateGradient(f, gd, temperature,
&potential,
QuadraticLineMinimizer));
const int numiters = 200;
for (int i=0;i<numiters && min.improve_energy(true);i++) {
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
fflush(stdout);
{
char* name = new char[1000];
sprintf(name, "papers/water-saft/figs/hughes-lj-%s-%gK-density-%d.eps", argv[1], temperature/kB, i);
Grid density(gd, EffectivePotentialToDensity()(temperature, gd, potential));
density.epsNativeSlice(name,
Cartesian(0,ymax,0), Cartesian(0,0,zmax),
Cartesian(0,ymax/2,zmax/2));
}
Grid gradient(gd, potential);
gradient *= 0;
f.integralgrad(temperature, potential, &gradient);
char* gradname = new char[1000];
sprintf(gradname, "papers/water-saft/figs/hughes-lj-%s-%gK-gradient-%d.eps", argv[1], temperature/kB, i);
gradient.epsNativeSlice(gradname,
Cartesian(0,ymax,0), Cartesian(0,0,zmax),
Cartesian(0,ymax/2,zmax/2));
Grid density(gd, EffectivePotentialToDensity()(temperature, gd, potential));
char *plotname = (char *)malloc(1024);
sprintf(plotname, "papers/water-saft/figs/hughes-lj-%s-%gK-%d.dat", argv[1], temperature/kB, i);
plot_grids_y_direction(plotname, density, gradient);
// Grid gradient(gd, potential);
// gradient *= 0;
// f.integralgrad(temperature, potential, &gradient);
// sprintf(name, "papers/water-saft/figs/lj-%s-%d-gradient-big.eps", argv[1], i);
// gradient.epsNativeSlice("papers/water-saft/figs/lj-gradient-big.eps",
// Cartesian(0,ymax,0), Cartesian(0,0,zmax),
// Cartesian(0,ymax/2,zmax/2));
// sprintf(name, "papers/water-saft/figs/lj-%s-%d-big.dat", argv[1], i);
// plot_grids_y_direction(name, density, gradient);
}
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
energy = min.energy();
printf("Total energy is %.15g\n", energy);
// Here we free the minimizer with its associated data structures.
}
{
double peak = peak_memory()/1024.0/1024;
double current = current_memory()/1024.0/1024;
printf("Peak memory use is %g M (current is %g M)\n", peak, current);
}
Grid gradient(gd, potential);
gradient *= 0;
f.integralgrad(temperature, potential, &gradient);
gradient.epsNativeSlice("papers/water-saft/figs/hughes-lj-gradient.eps",
Cartesian(0,ymax,0), Cartesian(0,0,zmax),
Cartesian(0,ymax/2,zmax/2));
double entropy = S.integral(temperature, potential);
Grid density(gd, EffectivePotentialToDensity()(temperature, gd, potential));
// Grid zeroed_out_density(gd, density.cwise()*constraint); // this is zero inside the sphere!
Grid X_values(gd, X(temperature, gd, density));
//Grid H_bonds_grid(gd, zeroed_out_density.cwise()*(4*(VectorXd::Ones(gd.NxNyNz)-X_values)));
//const double broken_H_bonds = (HB(temperature, n_1atm)/n_1atm)*zeroed_out_density.integrate() - H_bonds_grid.integrate();
//printf("Number of water molecules is %g\n", density.integrate());
printf("The bulk energy per cell should be %g\n", EperCell);
printf("The bulk energy based on number should be %g\n", EperNumber*density.integrate());
printf("The bulk entropy is %g/N\n", SperNumber);
Functional otherS = EntropySaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB,
hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling);
printf("The bulk entropy (haskell) = %g/N\n", otherS(temperature, n_1atm)/n_1atm);
//printf("My entropy is %g when I would expect %g\n", entropy, entropy - SperNumber*density.integrate());
double hentropy = otherS.integral(temperature, density);
otherS.print_summary(" ", hentropy, "total entropy");
printf("My haskell entropy is %g, when I would expect = %g, difference is %g\n", hentropy,
otherS(temperature, n_1atm)*density.integrate()/n_1atm,
hentropy - otherS(temperature, n_1atm)*density.integrate()/n_1atm);
FILE *o = fopen(datname, "w");
fprintf(o, "%g\t%.15g\t%.15g\t%.15g\n", temperature/kB, energy - EperNumber*density.integrate(),
temperature*(entropy - SperNumber*density.integrate()),
temperature*(hentropy - otherS(temperature, n_1atm)*density.integrate()/n_1atm));
fclose(o);
char *plotname = (char *)malloc(1024);
sprintf(plotname, "papers/water-saft/figs/hughes-lj-%s-%gK.dat", argv[1], temperature/kB);
//plot_grids_y_direction(plotname, density, X_values);
plot_grids_y_direction(plotname, density, gradient);
free(plotname);
double peak = peak_memory()/1024.0/1024;
printf("Peak memory use is %g M\n", peak);
double oldN = density.integrate();
density = n_1atm*VectorXd::Ones(gd.NxNyNz);;
double hentropyb = otherS.integral(temperature, density);
printf("bulklike thingy has %g molecules\n", density.integrate());
otherS.print_summary(" ", hentropyb, "bulk-like entropy");
printf("entropy difference is %g\n", hentropy - hentropyb*oldN/density.integrate());
clock_t end_time = clock();
double seconds = (end_time - start_time)/double(CLOCKS_PER_SEC);
double hours = seconds/60/60;
printf("Entire calculation took %.0f hours %.0f minutes\n", hours, 60*(hours-floor(hours)));
}
int main(int, char **) {
FILE *o = fopen("papers/hughes-saft/figs/single-rod-in-water-low-res.dat", "w");
Functional f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, 0));
double n_1atm = pressure_to_density(f, hughes_water_prop.kT, atmospheric_pressure,
0.001, 0.01);
double mu_satp = find_chemical_potential(f, hughes_water_prop.kT, n_1atm);
f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu_satp));
const double EperVolume = f(hughes_water_prop.kT, -hughes_water_prop.kT*log(n_1atm));
for (cavitysize=1.0*nm; cavitysize<=1.1*nm; cavitysize += 0.5*nm) {
Lattice lat(Cartesian(width,0,0), Cartesian(0,ymax,0), Cartesian(0,0,zmax));
GridDescription gd(lat, 0.5);
Grid potential(gd);
Grid constraint(gd);
constraint.Set(notinwall);
f = OfEffectivePotential(SaftFluid2(hughes_water_prop.lengthscale,
hughes_water_prop.epsilonAB, hughes_water_prop.kappaAB,
hughes_water_prop.epsilon_dispersion,
hughes_water_prop.lambda_dispersion,
hughes_water_prop.length_scaling, mu_satp));
f = constrain(constraint, f);
// constraint.epsNativeSlice("papers/hughes-saft/figs/single-rod-in-water-constraint.eps",
// Cartesian(0,ymax,0), Cartesian(0,0,zmax),
// Cartesian(0,ymax/2,zmax/2));
//printf("Constraint has become a graph!\n");
potential = hughes_water_prop.liquid_density*constraint
+ 1000*hughes_water_prop.vapor_density*VectorXd::Ones(gd.NxNyNz);
//potential = hughes_water_prop.liquid_density*VectorXd::Ones(gd.NxNyNz);
potential = -hughes_water_prop.kT*potential.cwise().log();
Minimizer min = Precision(1e-11, PreconditionedConjugateGradient(f, gd, hughes_water_prop.kT,
&potential,
QuadraticLineMinimizer));
//printf("\nDiameter of rod = %g bohr (%g nm)\n", cavitysize, cavitysize/nm);
const int numiters = 50;
for (int i=0;i<numiters && min.improve_energy(false);i++) {
fflush(stdout);
//Grid density(gd, EffectivePotentialToDensity()(hughes_water_prop.kT, gd, potential));
//density.epsNativeSlice("papers/hughes-saft/figs/single-rod-in-water.eps",
// Cartesian(0,ymax,0), Cartesian(0,0,zmax),
// Cartesian(0,ymax/2,zmax/2));
// sleep(3);
}
const double EperCell = EperVolume*(zmax*ymax - 0.25*M_PI*cavitysize*cavitysize)*width;
//printf("The bulk energy per cell should be %g\n", EperCell);
double energy = (min.energy() - EperCell)/width;
//printf("Energy is %.15g\n", energy);
fprintf(o, "%g\t%.15g\n", cavitysize/nm, energy);
char *plotname = (char *)malloc(1024);
sprintf(plotname, "papers/hughes-saft/figs/single-rod-res0.5-slice-%04.1f.dat", cavitysize/nm);
Grid density(gd, EffectivePotentialToDensity()(hughes_water_prop.kT, gd, potential));
plot_grids_y_direction(plotname, density);
free(plotname);
}
fclose(o);
}
