Commit 226ff24a authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Also updated the Minimal hydro scheme to the new cooling way

parent ef8184b8
import numpy as np
import matplotlib.pyplot as plt
import h5py as h5
import sys
stats_filename = "./energy.txt"
snap_filename = "coolingBox_000.hdf5"
#plot_dir = "./"
n_snaps = 41
time_end = 4.0
dt_snap = 0.1
#some constants in cgs units
k_b = 1.38E-16 #boltzmann
m_p = 1.67e-24 #proton mass
#initial conditions set in makeIC.py
rho = 4.8e3
P = 4.5e6
#n_H_cgs = 0.0001
gamma = 5./3.
T_init = 1.0e5
#find the sound speed
#Read the units parameters from the snapshot
f = h5.File(snap_filename,'r')
units = f["InternalCodeUnits"]
unit_mass = units.attrs["Unit mass in cgs (U_M)"]
unit_length = units.attrs["Unit length in cgs (U_L)"]
unit_time = units.attrs["Unit time in cgs (U_t)"]
parameters = f["Parameters"]
cooling_lambda = float(parameters.attrs["LambdaCooling:lambda_cgs"])
min_T = float(parameters.attrs["LambdaCooling:minimum_temperature"])
mu = float(parameters.attrs["LambdaCooling:mean_molecular_weight"])
X_H = float(parameters.attrs["LambdaCooling:hydrogen_mass_abundance"])
#get number of particles
header = f["Header"]
n_particles = header.attrs["NumPart_ThisFile"][0]
#read energy and time arrays
array = np.genfromtxt(stats_filename,skip_header = 1)
time = array[:,0]
total_energy = array[:,2]
total_mass = array[:,1]
time = time[1:]
total_energy = total_energy[1:]
total_mass = total_mass[1:]
#conversions to cgs
rho_cgs = rho * unit_mass / (unit_length)**3
time_cgs = time * unit_time
u_init_cgs = total_energy[0]/(total_mass[0]) * unit_length**2 / (unit_time)**2
n_H_cgs = X_H * rho_cgs / m_p
#find the sound speed in cgs
c_s = np.sqrt((gamma - 1.)*k_b*T_init/(mu*m_p))
#assume box size is unit length
sound_crossing_time = unit_length/c_s
print "Sound speed = %g cm/s" %c_s
print "Sound crossing time = %g s" %sound_crossing_time
#find the energy floor
u_floor_cgs = k_b * min_T / (mu * m_p * (gamma - 1.))
#find analytic solution
analytic_time_cgs = np.linspace(time_cgs[0],time_cgs[-1],1000)
du_dt_cgs = -cooling_lambda * n_H_cgs**2 / rho_cgs
u_analytic = du_dt_cgs*(analytic_time_cgs - analytic_time_cgs[0]) + u_init_cgs
cooling_time = u_init_cgs/(-du_dt_cgs)
#put time in units of sound crossing time
time=time_cgs/sound_crossing_time
analytic_time = analytic_time_cgs/sound_crossing_time
#rescale energy to initial energy
total_energy /= total_energy[0]
u_analytic /= u_init_cgs
u_floor_cgs /= u_init_cgs
# plot_title = r"$\Lambda \, = \, %1.1g \mathrm{erg}\mathrm{cm^3}\mathrm{s^{-1}} \, \, T_{init} = %1.1g\mathrm{K} \, \, T_{floor} = %1.1g\mathrm{K} \, \, n_H = %1.1g\mathrm{cm^{-3}}$" %(cooling_lambda,T_init,T_floor,n_H)
# plot_filename = "energy_plot_creasey_no_cooling_T_init_1p0e5_n_H_0p1.png"
#analytic_solution = np.zeros(n_snaps-1)
for i in range(u_analytic.size):
if u_analytic[i]<u_floor_cgs:
u_analytic[i] = u_floor_cgs
plt.plot(time-time[0],total_energy,'k',label = "Numerical solution from energy.txt")
plt.plot(analytic_time-analytic_time[0],u_analytic,'r',lw = 2.0,label = "Analytic Solution")
#now get energies from the snapshots
snapshot_time = np.linspace(0,time_end,num = n_snaps)
snapshot_time = snapshot_time[1:]
snapshot_time_cgs = snapshot_time * unit_time
snapshot_time = snapshot_time_cgs/ sound_crossing_time
snapshot_time -= snapshot_time[0]
snapshot_energy = np.zeros(n_snaps)
for i in range(0,n_snaps):
snap_filename = "coolingBox_%03d.hdf5" %i
f = h5.File(snap_filename,'r')
snapshot_internal_energy_array = np.array(f["PartType0/InternalEnergy"])
total_internal_energy = np.sum(snapshot_internal_energy_array)
velocity_array = np.array(f["PartType0/Velocities"])
total_kinetic_energy = 0.5*np.sum(velocity_array**2)
snapshot_energy[i] = total_internal_energy + total_kinetic_energy
snapshot_energy/=snapshot_energy[0]
snapshot_energy = snapshot_energy[1:]
plt.plot(snapshot_time,snapshot_energy,'bd',label = "Numerical solution from snapshots")
#plt.title(r"$n_H = %1.1e \, \mathrm{cm}^{-3}$" %n_H_cgs)
plt.xlabel("Time (sound crossing time)")
plt.ylabel("Energy/Initial energy")
plt.ylim(0.99,1.01)
#plt.xlim(0,min(10,time[-1]))
plt.legend(loc = "upper right")
if (int(sys.argv[1])==0):
plt.show()
else:
plt.savefig(full_plot_filename,format = "png")
plt.close()
...@@ -49,26 +49,22 @@ ...@@ -49,26 +49,22 @@
* energy from the thermodynamic variable. * energy from the thermodynamic variable.
* *
* @param p The particle of interest * @param p The particle of interest
* @param dt Time since the last kick
*/ */
__attribute__((always_inline)) INLINE static float hydro_get_internal_energy( __attribute__((always_inline)) INLINE static float hydro_get_internal_energy(
const struct part *restrict p, float dt) { const struct part *restrict p) {
return p->u + p->u_dt * dt; return p->u;
} }
/** /**
* @brief Returns the pressure of a particle * @brief Returns the pressure of a particle
* *
* @param p The particle of interest * @param p The particle of interest
* @param dt Time since the last kick
*/ */
__attribute__((always_inline)) INLINE static float hydro_get_pressure( __attribute__((always_inline)) INLINE static float hydro_get_pressure(
const struct part *restrict p, float dt) { const struct part *restrict p) {
const float u = p->u + p->u_dt * dt;
return gas_pressure_from_internal_energy(p->rho, u); return gas_pressure_from_internal_energy(p->rho, p->u);
} }
/** /**
...@@ -79,24 +75,20 @@ __attribute__((always_inline)) INLINE static float hydro_get_pressure( ...@@ -79,24 +75,20 @@ __attribute__((always_inline)) INLINE static float hydro_get_pressure(
* the thermodynamic variable. * the thermodynamic variable.
* *
* @param p The particle of interest * @param p The particle of interest
* @param dt Time since the last kick
*/ */
__attribute__((always_inline)) INLINE static float hydro_get_entropy( __attribute__((always_inline)) INLINE static float hydro_get_entropy(
const struct part *restrict p, float dt) { const struct part *restrict p) {
const float u = p->u + p->u_dt * dt;
return gas_entropy_from_internal_energy(p->rho, u); return gas_entropy_from_internal_energy(p->rho, p->u);
} }
/** /**
* @brief Returns the sound speed of a particle * @brief Returns the sound speed of a particle
* *
* @param p The particle of interest * @param p The particle of interest
* @param dt Time since the last kick
*/ */
__attribute__((always_inline)) INLINE static float hydro_get_soundspeed( __attribute__((always_inline)) INLINE static float hydro_get_soundspeed(
const struct part *restrict p, float dt) { const struct part *restrict p) {
return p->force.soundspeed; return p->force.soundspeed;
} }
...@@ -124,68 +116,31 @@ __attribute__((always_inline)) INLINE static float hydro_get_mass( ...@@ -124,68 +116,31 @@ __attribute__((always_inline)) INLINE static float hydro_get_mass(
} }
/** /**
* @brief Modifies the thermal state of a particle to the imposed internal * @brief Returns the time derivative of internal energy of a particle
* energy
* *
* This overwrites the current state of the particle but does *not* change its * We assume a constant density.
* time-derivatives. Internal energy, pressure, sound-speed and signal velocity
* will be updated.
* *
* @param p The particle * @param p The particle of interest
* @param u The new internal energy
*/ */
__attribute__((always_inline)) INLINE static void hydro_set_internal_energy( __attribute__((always_inline)) INLINE static float hydro_get_internal_energy_dt(
struct part *restrict p, float u) { const struct part *restrict p) {
p->u = u;
/* Compute the new pressure */
const float pressure = gas_pressure_from_internal_energy(p->rho, p->u);
/* Compute the new sound speed */
const float soundspeed = gas_soundspeed_from_internal_energy(p->rho, p->u);
/* Update the signal velocity */
const float v_sig_old = p->force.v_sig;
const float v_sig_new = p->force.v_sig - p->force.soundspeed + soundspeed;
const float v_sig = max(v_sig_old, v_sig_new);
p->force.soundspeed = soundspeed; return p->u_dt;
p->force.pressure = pressure;
p->force.v_sig = v_sig;
} }
/** /**
* @brief Modifies the thermal state of a particle to the imposed entropy * @brief Returns the time derivative of internal energy of a particle
* *
* This overwrites the current state of the particle but does *not* change its * We assume a constant density.
* time-derivatives. Internal energy, pressure, sound-speed and signal velocity
* will be updated.
* *
* @param p The particle * @param p The particle of interest.
* @param S The new entropy * @param du_dt The new time derivative of the internal energy.
*/ */
__attribute__((always_inline)) INLINE static void hydro_set_entropy( __attribute__((always_inline)) INLINE static void hydro_set_internal_energy_dt(
struct part *restrict p, float S) { struct part *restrict p, float du_dt) {
p->u = gas_internal_energy_from_entropy(p->rho, S);
/* Compute the pressure */ p->u_dt = du_dt;
const float pressure = gas_pressure_from_internal_energy(p->rho, p->u);
/* Compute the new sound speed */
const float soundspeed = gas_soundspeed_from_internal_energy(p->rho, p->u);
/* Update the signal velocity */
const float v_sig_old = p->force.v_sig;
const float v_sig_new = p->force.v_sig - p->force.soundspeed + soundspeed;
const float v_sig = max(v_sig_old, v_sig_new);
p->force.soundspeed = soundspeed;
p->force.pressure = pressure;
p->force.v_sig = v_sig;
} }
/** /**
* @brief Computes the hydro time-step of a given particle * @brief Computes the hydro time-step of a given particle
* *
...@@ -406,10 +361,7 @@ __attribute__((always_inline)) INLINE static void hydro_kick_extra( ...@@ -406,10 +361,7 @@ __attribute__((always_inline)) INLINE static void hydro_kick_extra(
/* Do not decrease the energy by more than a factor of 2*/ /* Do not decrease the energy by more than a factor of 2*/
const float u_change = p->u_dt * dt; const float u_change = p->u_dt * dt;
if (u_change > -0.5f * xp->u_full) xp->u_full = max(xp->u_full + u_change, 0.5f * xp->u_full);
xp->u_full += u_change;
else
xp->u_full *= 0.5f;
/* Compute the pressure */ /* Compute the pressure */
const float pressure = gas_pressure_from_internal_energy(p->rho, xp->u_full); const float pressure = gas_pressure_from_internal_energy(p->rho, xp->u_full);
......
...@@ -71,12 +71,12 @@ void hydro_read_particles(struct part* parts, struct io_props* list, ...@@ -71,12 +71,12 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
float convert_S(struct engine* e, struct part* p) { float convert_S(struct engine* e, struct part* p) {
return hydro_get_entropy(p, 0); return hydro_get_entropy(p);
} }
float convert_P(struct engine* e, struct part* p) { float convert_P(struct engine* e, struct part* p) {
return hydro_get_pressure(p, 0); return hydro_get_pressure(p);
} }
/** /**
......
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