コード例 #1
0
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);
}
コード例 #2
0
ファイル: four-rods-in-water.cpp プロジェクト: droundy/deft
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);
  }
}
コード例 #3
0
ファイル: sphere.cpp プロジェクト: droundy/deft
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)));
}
コード例 #4
0
ファイル: box.cpp プロジェクト: Chris-Haglund/deft
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);
}
コード例 #5
0
ファイル: hughes-lj-atom.cpp プロジェクト: droundy/deft
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)));
}
コード例 #6
0
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);
}