static void took(const char *name) {
static clock_t last_time = clock();
clock_t t = clock();
assert(name); // so it'll count as being used...
double peak = peak_memory()/1024.0/1024;
printf("\t\t%s took %g seconds (peak memory: %g M)\n", name, (t-last_time)/double(CLOCKS_PER_SEC), peak);
last_time = t;
}
double check_peak(const char *name, const char *name2, FILE *out,
double peakmin, double peakmax,
double cpu = 0, double cpurat = 1.6) {
printf("===> Testing %s of %s <===\n", name, name2);
double cputime = get_time() - last_time;
double peak = peak_memory()/1024.0/1024;
if (cpu)
printf("CPU time is %g s (%.0f%%, with memory use %.0f M)\n", cputime, (cputime - cpu)/cpu*100, peak);
else
printf("CPU time is %g s (with memory use %.0f M)\n", cputime, peak);
if (peak < peakmin) {
printf("FAIL: Peak memory use of %s %s should be at least %g (but it's %g)!\n", name, name2, peakmin, peak);
retval++;
}
if (peak > peakmax) {
printf("FAIL: Peak memory use of %s %s should be under %g (but it's %g)!\n", name, name2, peakmax, peak);
retval++;
}
if (cpu) {
if (cputime < cpu/cpurat) {
printf("OOPS: CPU time of %s %s should be at least %g!\n", name, name2, cpu/cpurat);
//retval++;
numoops++;
}
if (cputime > cpu*cpurat) {
printf("OOPS: CPU time of %s %s should be under %g!\n", name, name2, cpu*cpurat);
//retval++;
numoops++;
}
}
if (out) {
fprintf(out, "%g\t%g\n", peak, cputime);
fflush(out);
}
reset_peak_memory();
last_time = get_time();
return cputime;
}
void run_with_eta(double eta, const char *name, Functional fhs) {
// Generates a data file for the pair distribution function, for filling fraction eta
// and distance of first sphere from wall of z0. Data saved in a table such that the
// columns are x values and rows are z1 values.
printf("Now starting run_with_eta with eta = %g name = %s\n",
eta, name);
Functional f = OfEffectivePotential(fhs + IdealGas());
double mu = find_chemical_potential(f, 1, eta/(4*M_PI/3));
f = OfEffectivePotential(fhs + IdealGas()
+ ChemicalPotential(mu));
Lattice lat(Cartesian(width,0,0), Cartesian(0,width,0), Cartesian(0,0,width));
GridDescription gd(lat, dx);
Grid potential(gd);
Grid constraint(gd);
constraint.Set(notinsphere);
f = constrain(constraint, f);
potential = (eta*constraint + 1e-4*eta*VectorXd::Ones(gd.NxNyNz))/(4*M_PI/3);
potential = -potential.cwise().log();
const double approx_energy = (fhs + IdealGas() + ChemicalPotential(mu))(1, eta/(4*M_PI/3))*uipow(width,3);
const double precision = fabs(approx_energy*1e-10);
//printf("Minimizing to %g absolute precision...\n", precision);
{ // Put mimizer in block so as to free it when we finish minimizing to save memory.
Minimizer min = Precision(precision,
PreconditionedConjugateGradient(f, gd, 1,
&potential,
QuadraticLineMinimizer));
for (int i=0;min.improve_energy(true) && i<100;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);
}
took("Doing the minimization");
}
Grid density(gd, EffectivePotentialToDensity()(1, gd, potential));
Grid gsigma(gd, gSigmaA(1.0)(1, gd, density));
Grid nA(gd, ShellConvolve(2)(1, density)/(4*M_PI*4));
Grid n3(gd, StepConvolve(1)(1, density));
Grid nbar_sokolowski(gd, StepConvolve(1.6)(1, density));
nbar_sokolowski /= (4.0/3.0*M_PI*ipow(1.6, 3));
// Create the walls directory if it doesn't exist.
if (mkdir("papers/pair-correlation/figs/walls", 0777) != 0 && errno != EEXIST) {
// We failed to create the directory, and it doesn't exist.
printf("Failed to create papers/pair-correlation/figs/walls: %s",
strerror(errno));
exit(1); // fail immediately with error code
}
// here you choose the values of z0 to use
// dx is the resolution at which we compute the density.
char *plotname = new char[4096];
for (double z0 = 2.1; z0 < 4.5; z0 += 2.1) {
// For each z0, we now pick one of our methods for computing the
// pair distribution function:
for (int version = 0; version < numplots; version++) {
sprintf(plotname,
"papers/pair-correlation/figs/triplet%s-%s-%04.2f-%1.2f.dat",
name, fun[version], eta, z0);
FILE *out = fopen(plotname,"w");
FILE *xfile = fopen("papers/pair-correlation/figs/triplet-x.dat","w");
FILE *zfile = fopen("papers/pair-correlation/figs/triplet-z.dat","w");
// the +1 for z0 and z1 are to shift the plot over, so that a sphere touching the wall
// is at z = 0, to match with the monte carlo data
const Cartesian r0(0,0,z0);
for (double x = 0; x < 4; x += dx) {
for (double z1 = -4; z1 <= 9; z1 += dx) {
const Cartesian r1(x,0,z1);
double g2 = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out, "%g\t", g3);
fprintf(xfile, "%g\t", x);
fprintf(zfile, "%g\t", z1);
}
fprintf(out, "\n");
fprintf(xfile, "\n");
fprintf(zfile, "\n");
}
fclose(out);
fclose(xfile);
fclose(zfile);
}
}
delete[] plotname;
took("Dumping the triplet dist plots");
const double ds = 0.01; // step size to use in path plots, FIXME increase for publication!
const double delta = .1; //this is the value of radius of the
//particle as it moves around the contact
//sphere on its path
char *plotname_path = new char[4096];
for (int version = 0; version < numplots; version++) {
sprintf(plotname_path,
"papers/pair-correlation/figs/triplet%s-path-%s-%04.2f.dat",
name, fun[version], eta);
FILE *out_path = fopen(plotname_path, "w");
if (!out_path) {
fprintf(stderr, "Unable to create file %s!\n", plotname_path);
return;
}
sprintf(plotname_path,
"papers/pair-correlation/figs/triplet-back-contact-%s-%04.2f.dat",
fun[version], eta);
FILE *out_back = fopen(plotname_path, "w");
if (!out_back) {
fprintf(stderr, "Unable to create file %s!\n", plotname_path);
return;
}
fprintf(out_path, "# unused\tg3\tz\tx\n");
fprintf(out_back, "# unused\tg3\tz\tx\n");
const Cartesian r0(0,0, 2.0+delta);
const double max_theta = M_PI*2.0/3;
for (double z = 7; z >= 2*(2.0 + delta); z-=ds) {
const Cartesian r1(0,0,z);
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_path,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
for (double z = -7; z <= -(2.0 + delta); z+=ds) {
const Cartesian r1(0,0,z);
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_back,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
const double dtheta = ds/2;
for (double theta = 0; theta <= max_theta; theta += dtheta){
const Cartesian r1((2.0+delta)*sin(theta), 0, (2.0+delta)*(1+cos(theta)));
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_path,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
for (double theta = 0; theta <= max_theta; theta += dtheta){
const Cartesian r1((2.0+delta)*sin(theta), 0,-(2.0+delta)*cos(theta));
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_back,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
for (double x = (2.0+delta)*sqrt(3)/2; x<=6; x+=ds){
const Cartesian r1(x, 0, 1.0+delta/2);
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_path,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
fprintf(out_back,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
fclose(out_path);
fclose(out_back);
}
for (int version = 0; version < numplots; version++) {
sprintf(plotname_path,
"papers/pair-correlation/figs/triplet-path-inbetween-%s-%04.2f.dat",
fun[version], eta);
FILE *out_path = fopen(plotname_path, "w");
if (!out_path) {
fprintf(stderr, "Unable to create file %s!\n", plotname_path);
return;
}
sprintf(plotname_path,
"papers/pair-correlation/figs/triplet-back-inbetween-%s-%04.2f.dat",
fun[version], eta);
FILE *out_back = fopen(plotname_path, "w");
if (!out_back) {
fprintf(stderr, "Unable to create file %s!\n", plotname_path);
return;
}
fprintf(out_path, "# unused\tg3\tz\tx\n");
fprintf(out_back, "# unused\tg3\tz\tx\n");
const Cartesian r0(0,0, 4.0+2*delta);
const double max_theta = M_PI;
for (double z = 11; z >= 3*(2.0 + delta); z-=ds) {
const Cartesian r1(0,0,z);
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_path,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
for (double z = -10; z <= -(2.0 + delta); z+=ds) {
const Cartesian r1(0,0,z);
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_back,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
const double dtheta = ds/2;
for (double theta = 0; theta <= max_theta; theta += dtheta){
const Cartesian r1((2.0+delta)*sin(theta), 0, (2.0+delta)*(2+cos(theta)));
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_path,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
for (double theta = 0; theta <= max_theta; theta += dtheta){
const Cartesian r1((2.0+delta)*sin(theta), 0, -(2.0+delta)*cos(theta));
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_back,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
for (double x = 0; x>=-6; x-=ds){
const Cartesian r1(x, 0, 2.0+delta);
double g2_path = pairdists[version](gsigma, density, nA, n3, nbar_sokolowski, r0, r1);
double n_bulk = (3.0/4.0/M_PI)*eta;
double g3 = g2_path*density(r0)*density(r1)/n_bulk/n_bulk;
fprintf(out_path,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
fprintf(out_back,"0\t%g\t%g\t%g\n", g3, r1[2], r1[0]);
}
fclose(out_path);
fclose(out_back);
}
delete[] plotname_path;
}
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, char **) {
for (double eta = 0.3; eta < 0.35; eta += 0.1) {
// Generates a data file for the pair distribution function, for filling fraction eta
// and distance of first sphere from wall of z0. Data saved in a table such that the
// columns are x values and rows are z1 values.
printf("Now starting sphere_with_wall with eta = %g\n",eta);
Lattice lat(Cartesian(width,0,0), Cartesian(0,width,0), Cartesian(0,0,width+2*spacing));
GridDescription gd(lat, dx); //the resolution here dramatically affects our memory use
Functional f = OfEffectivePotential(WB + IdealGas());
double mu = find_chemical_potential(f, 1, eta/(4*M_PI/3));
f = OfEffectivePotential(WB + IdealGas()
+ ChemicalPotential(mu));
Grid potential(gd);
Grid constraint(gd);
constraint.Set(*notinwall_or_sphere);
constraint.epsNativeSlice("myconstraint.eps",
Cartesian(0, 0, 2*(width+2*spacing)),
Cartesian(2*width, 0, 0),
Cartesian(0, 0, 0));
f = constrain(constraint, f);
potential = (eta*constraint + 1e-4*eta*VectorXd::Ones(gd.NxNyNz))/(4*M_PI/3);
potential = -potential.cwise().log();
const double approx_energy = (WB + IdealGas() + ChemicalPotential(mu))(1, eta/(4*M_PI/3))*dw*dw*width;
const double precision = fabs(approx_energy*1e-4);
//printf("Minimizing to %g absolute precision...\n", precision);
Minimizer min = Precision(precision,
PreconditionedConjugateGradient(f, gd, 1,
&potential,
QuadraticLineMinimizer));
{
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);
}
for (int i=0; min.improve_energy(true) && i<100; 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);
}
Grid density(gd, EffectivePotentialToDensity()(1, gd, potential));
char *plotname = new char[1024];
sprintf(plotname, "papers/pair-correlation/figs/walls/wallsWB-sphere-dft-%04.2f.dat", eta);
pair_plot(plotname, density);
delete[] plotname;
char *plotname_path = new char[1024];
sprintf(plotname_path, "papers/pair-correlation/figs/walls/wallsWB-sphere-dft-path-%04.2f.dat", eta);
path_plot(plotname_path, density, constraint);
delete[] plotname_path;
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);
fflush(stdout);
}
fflush(stdout);
}
fflush(stdout);
// Just create this file so make knows we have run.
if (!fopen("papers/pair-correlation/figs/walls_sphere.dat", "w")) {
printf("Error creating walls.dat!\n");
return 1;
}
fflush(stdout);
return 1;
}
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)));
}
