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Commit 226ff24a authored by Matthieu Schaller's avatar Matthieu Schaller
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Also updated the Minimal hydro scheme to the new cooling way

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examples/CoolingBox/test_energy_conservation.py deleted 100644 → 0
View file @ 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()
src/hydro/Minimal/hydro.h
View file @ 226ff24a
......@@ -49,26 +49,22 @@
* energy from the thermodynamic variable.
*
* @param p The particle of interest
* @param dt Time since the last kick
*/
__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
*
* @param p The particle of interest
* @param dt Time since the last kick
*/
__attribute__((always_inline)) INLINE static float hydro_get_pressure(
const struct part *restrict p, float dt) {
const float u = p->u + p->u_dt * dt;
const struct part *restrict p) {
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(
* the thermodynamic variable.
*
* @param p The particle of interest
* @param dt Time since the last kick
*/
__attribute__((always_inline)) INLINE static float hydro_get_entropy(
const struct part *restrict p, float dt) {
const float u = p->u + p->u_dt * dt;
const struct part *restrict p) {
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
*
* @param p The particle of interest
* @param dt Time since the last kick
*/
__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;
}
......@@ -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
* energy
* @brief Returns the time derivative of internal energy of a particle
*
* This overwrites the current state of the particle but does *not* change its
* time-derivatives. Internal energy, pressure, sound-speed and signal velocity
* will be updated.
* We assume a constant density.
*
* @param p The particle
* @param u The new internal energy
* @param p The particle of interest
*/
__attribute__((always_inline)) INLINE static void hydro_set_internal_energy(
struct part *restrict p, float u) {
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);
__attribute__((always_inline)) INLINE static float hydro_get_internal_energy_dt(
const struct part *restrict p) {
p->force.soundspeed = soundspeed;
p->force.pressure = pressure;
p->force.v_sig = v_sig;
return p->u_dt;
}
/**
* @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
* time-derivatives. Internal energy, pressure, sound-speed and signal velocity
* will be updated.
* We assume a constant density.
*
* @param p The particle
* @param S The new entropy
* @param p The particle of interest.
* @param du_dt The new time derivative of the internal energy.
*/
__attribute__((always_inline)) INLINE static void hydro_set_entropy(
struct part *restrict p, float S) {
p->u = gas_internal_energy_from_entropy(p->rho, S);
__attribute__((always_inline)) INLINE static void hydro_set_internal_energy_dt(
struct part *restrict p, float du_dt) {
/* Compute the 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;
p->force.pressure = pressure;
p->force.v_sig = v_sig;
p->u_dt = du_dt;
}
/**
* @brief Computes the hydro time-step of a given particle
*
......@@ -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*/
const float u_change = p->u_dt * dt;
if (u_change > -0.5f * xp->u_full)
xp->u_full += u_change;
else
xp->u_full *= 0.5f;
xp->u_full = max(xp->u_full + u_change, 0.5f * xp->u_full);
/* Compute the pressure */
const float pressure = gas_pressure_from_internal_energy(p->rho, xp->u_full);
......
src/hydro/Minimal/hydro_io.h
View file @ 226ff24a
......@@ -71,12 +71,12 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
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) {
return hydro_get_pressure(p, 0);
return hydro_get_pressure(p);
}
/**
......
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