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Improved output and config

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This commit is contained in:
Yohai Meiron 2020-03-31 22:06:04 -04:00
parent 5cb4282be4
commit 62b0d7e491
6 changed files with 126 additions and 107 deletions
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1
.gitignore vendored
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@ -8,3 +8,4 @@
*.mask
grapite-dev-exec-threshold
phigrape
*.h5

6
config.cpp
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@ -151,8 +151,14 @@ Config::Config(std::string file_name)
dt_contr = get_parameter<double>(dictionary, "dt_contr");
dt_bh = get_parameter<double>(dictionary, "dt_bh", dt_contr);
eta = get_parameter<double>(dictionary, "eta");
input_file_name = get_parameter<std::string>(dictionary, "input_file_name", "data.con");
output_hdf5 = get_parameter<bool>(dictionary, "output_hdf5", false);
output_hdf5_double_precision = get_parameter<bool>(dictionary, "output_hdf5_double_precision", true);
output_ascii_precision = get_parameter<int>(dictionary, "output_ascii_precision", 10);
output_extra_mode = get_parameter<int>(dictionary, "output_extra_mode", 10);
dt_min_warning = get_parameter<bool>(dictionary, "dt_min_warning", false);
live_smbh_count = get_parameter<int>(dictionary, "live_smbh_count", 0);

3
config.h
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@ -15,6 +15,9 @@ public:
double eta;
std::string input_file_name;
bool output_hdf5;
bool output_hdf5_double_precision;
int output_ascii_precision;
int output_extra_mode;
bool dt_min_warning;
int live_smbh_count;
double live_smbh_custom_eps;

14
io.cpp
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@ -142,7 +142,7 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
#endif
}
void h5_write(const std::string file_name, const int step_num, const int N, const double t, const double *m, const double3 *x, const double3 *v, const double *pot, const double3 *acc, const double3 *jrk, const int write_mode=0, const bool use_double_precision=true)
void h5_write(const std::string file_name, const int step_num, const int N, const double t, const double *m, const double3 *x, const double3 *v, const double *pot, const double3 *acc, const double3 *jrk, const int extra_mode=0, const bool use_double_precision=true)
{
#ifdef HAS_HDF5
hid_t file_id, group_id, attribute_id, dataset_id, dataspace_id;
@ -151,13 +151,7 @@ void h5_write(const std::string file_name, const int step_num, const int N, cons
hid_t h5_float_type;
if (use_double_precision) h5_float_type = H5T_IEEE_F64LE;
else h5_float_type = H5T_IEEE_F32LE;
// static int zzz = 5;
file_id = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// file_id = H5Fcreate(std::to_string(zzz).c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// zzz++;
char group_name[32];
sprintf(group_name, "/Step#%d", step_num);
group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@ -180,9 +174,9 @@ void h5_write(const std::string file_name, const int step_num, const int N, cons
write_dataset("X", 2, (double*)x);
write_dataset("V", 2, (double*)v);
bool write_pot = (write_mode ) % 2;
bool write_acc = (write_mode >> 1) % 2;
bool write_jrk = (write_mode >> 2) % 2;
bool write_pot = (extra_mode ) % 2;
bool write_acc = (extra_mode >> 1) % 2;
bool write_jrk = (extra_mode >> 2) % 2;
if (write_pot) write_dataset("POT", 1, (double*)pot);
if (write_acc) write_dataset("ACC", 2, (double*)acc);
if (write_jrk) write_dataset("JRK", 2, (double*)jrk);

188
phigrape.conf
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@ -8,8 +8,8 @@ eps = 1E-4
# End time of the calculation
t_end = 0.25
# Interval of snapshot files output (xxxxxx.dat)
dt_disk = 1.0
# Interval of snapshot files output
dt_disk = 0.125
# Interval for the energy control output (contr.dat)
dt_contr = 0.125
@ -20,100 +20,132 @@ dt_bh = 0.125
# Parameter for timestep determination
eta = 0.01
# Name of the input file; use "data.con" in most cases
# Name of the input file; use "data.con" in most cases [default: data.con]
input_file_name = data.con
output_hdf5 = true
##### NOT IMPLEMENTED #######################
dt_min_warning = false
#############################################
##########
# OUTPUT #
##########
# Whether to use HDF5 format for snapshot and restart; regular ASCII snapshorts are saved if false [default: false]
#output_hdf5 = true
# If using HDF5 output, use double precision or not [default: true]
# Consider setting to false to save disk space. Restart file is always saved in double precision.
#output_hdf5_double_precision = true
# If using ASCII output, the number of digits after the decimal point [default: 10]
# Restart file is saved with 16 digits after the decimal point.
#output_ascii_precision = 6
# Extra output: optionally save potential, acceleration and jerk in snapshot files [default: 0]
# This is a number between 0 and 7 that encodes the output options in the following way:
# [value] = [save jerk]*4 + [save acceleration]*2 + [save potential]
# Example: choose 5 if it is needed to save the jerk and the potential, but not the acceleration for some reason.
# Currently implemented in HDF5 output only.
#output_extra_mode = 7
# Whether to output a warning on the screen when the minimum time step is encountered. [default: false]
#dt_min_warning = false
####################
# EXTERNAL GRAVITY #
####################
ext_units_physical = false
#unit_mass = 1e5
#unit_length = 10
# TODO add the option to normalize using other units
# Remember that external gravity models are applied at the same coordinate system as the particles. If the idea is to simulate a globular cluster orbiting in an external field, be sure to set the initial conditions appropriately (applying a shift to the coordinates and velocities).
# Notice that if physical units are used, the "a" and "b" parameters are in kiloparsec, not parsec!
# Whether the parameters for the external gravitational field given below are in physical units or Hénon units. If true, the system used is {kiloparsec, solar mass, kilometre per second} [default: false]
#ext_units_physical = true
ext_m_bulge = 0
ext_b_bulge = 0
ext_m_disk = 0
ext_a_disk = 0
ext_b_disk = 0
ext_m_halo_plummer = 0
ext_b_halo_plummer = 0
ext_log_halo_v = 0
# here the length scale for the logarithmic halo is in kpc, not pc like in the old phigrape.
ext_log_halo_r = 0
# If Physical units were selected, specify the simulation's unit mass (is solar masses) and unit lenght (in parsec; not kiloparsec)
# TODO: add the option to normalize using other units.
#unit_mass = 4E5 # MSun
#unit_length = 15 # pc
# The bulge is a Plummer potential with the following total mass and radius.
#ext_m_bulge = 5E9 # MSun
#ext_b_bulge = 1.9 # kpc
# The disk is a Miyamoto-Nagai potential with the following total mass, scale length, and scale height
#ext_m_disk = 6.8E10 # MSun
#ext_a_disk = 3.00 # kpc
#ext_b_disk = 0.28 # kpc
# This halo option is yet another Plummer potential with the following total mass and radius.
#ext_m_halo_plummer = 8E11 # MSun
#ext_b_halo_plummer = 245 # kpc
# This halo option is a logarithmic potential with the following velocity and radius parameters.
#ext_log_halo_v = 240 # km/s
#ext_log_halo_r = 1 # kpc
####################################
## LIVE SUPERMASSIVE BLACK HOLE(S) #
####################################
#
## There is special treatment for particles representing supermassive black holes (SMBHs): they are integrated at every time step, they can have custom softening in SMBH-SMBH interactions, and post Newtonian terms can be added to the gravity.
#
## The number of SMBH particles. Can be 0 (no SMBH), 1, or 2. [default: 0]
#live_smbh_count = 0
#
## Custom softening length for SMBH-SMBH interactions (can also be zero). If non-negative, the custom softening is applied. [default: -1]
###################################
# LIVE SUPERMASSIVE BLACK HOLE(S) #
###################################
# There is special treatment for particles representing supermassive black holes (SMBHs): they are integrated at every time step, they can have custom softening in SMBH-SMBH interactions, and post Newtonian terms can be added to the gravity.
# The number of SMBH particles. Can be 0 (no SMBH), 1, or 2. [default: 0]
#live_smbh_count = 2
# Custom softening length for SMBH-SMBH interactions (can also be zero). If non-negative, the custom softening is applied. [default: -1]
#live_smbh_custom_eps = 0
#
## Output additional diagnostics about live SMBHs. [default: false]
##TODO# dt_bh
# Output additional diagnostics about live SMBHs. [default: false]
#live_smbh_output = true
#
## Output additional diagnostics about the SMBH's (or SMBHs') nearest neighbours (number could be set as shown below). [default: false]
# Output additional diagnostics about the SMBH's (or SMBHs') nearest neighbours (number could be set as shown below). [default: false]
#live_smbh_neighbor_output = true
#
## Number of nearest neighbours to the SMBH (or SMBHs) to include in output. [default: 10]
# Number of nearest neighbours to the SMBH (or SMBHs) to include in output. [default: 10]
#live_smbh_neighbor_number = 10
#
###################################
## BINARY SUPERMASSIVE BLACK HOLE #
###################################
#
## The following parameters can be set when `live_smbh_count` is 2.
#
## Output additional diagnostics about the SMBH's sphere of influence (size could be set as shown below). [default: false]
##################################
# BINARY SUPERMASSIVE BLACK HOLE #
##################################
# The following parameters can be set when live_smbh_count is 2.
# Output additional diagnostics about the sphere of influence (size could be set as shown below). [default: false]
#binary_smbh_influence_sphere_output = true
#
## The influence sphere is centred at the binary SMBH's centre of mass, and its radius is the semi-major axis of the binary times the factor below. [default: 10.0]
#binary_smbh_influence_radius_factor = 3.162277660168379497918067e+03
#
## Add post Newtonian terms to SMBH-SMBH gravity. [default: false]
# The influence sphere is centred at the binary SMBH's centre of mass, and its radius is the semi-major axis of the binary times the factor below. [default: 10]
#binary_smbh_influence_radius_factor = 10
# Add post Newtonian terms to SMBH-SMBH gravity. [default: false]
#binary_smbh_pn = true
#
## A mask array (zeros and ones) determining whether or not to use specific post-Newtonian terms.
## The elements represent {0, 1, 2, 2.5, 3, 3.5, spin}
# A mask array (zeros and ones) determining whether or not to use specific post-Newtonian terms.
# The elements represent {0, 1, 2, 2.5, 3, 3.5, spin} [default: {1,1,1,1,1,1,1}]
#pn_usage = {1, 1, 1, 1, 0, 0, 0}
#
## The speed of light in N-body units [default: 500]
# The speed of light in N-body units [default: 500]
#pn_c = 477.12
#
#####################################
## Negative powers of two #
#####################################
## -1 1/2 0.5 #
## -2 1/4 0.25 #
## -3 1/8 0.125 #
## -4 1/16 0.0625 #
## -5 1/32 0.03125 #
## -6 1/64 0.015625 #
## -7 1/128 0.0078125 #
## -8 1/256 0.00390625 #
## -9 1/512 0.001953125 #
## -10 1/1024 0.0009765625 #
## -11 1/2048 0.00048828125 #
## -12 1/4096 0.000244140625 #
## -13 1/8192 0.0001220703125 #
## -14 1/16384 0.00006103515625 #
## -15 1/32768 0.000030517578125 #
## -16 1/65536 0.0000152587890625 #
#####################################
####################################
# Negative powers of two #
####################################
# -1 1/2 0.5 #
# -2 1/4 0.25 #
# -3 1/8 0.125 #
# -4 1/16 0.0625 #
# -5 1/32 0.03125 #
# -6 1/64 0.015625 #
# -7 1/128 0.0078125 #
# -8 1/256 0.00390625 #
# -9 1/512 0.001953125 #
# -10 1/1024 0.0009765625 #
# -11 1/2048 0.00048828125 #
# -12 1/4096 0.000244140625 #
# -13 1/8192 0.0001220703125 #
# -14 1/16384 0.00006103515625 #
# -15 1/32768 0.000030517578125 #
# -16 1/65536 0.0000152587890625 #
####################################

21
phigrape.cpp
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@ -291,22 +291,6 @@ void get_CPU_time(double *time_real, double *time_user, double *time_syst)
*time_user = *time_real;
}
void write_snap_data(char out_fname[], int diskstep, int N, double time_cur, int ind[], double m[], double3 x[], double3 v[])
{
auto out = fopen(out_fname, "w");
fprintf(out,"%06d \n", diskstep);
fprintf(out,"%07d \n", N);
fprintf(out,"%.10E \n", time_cur);
for (int i=0; i<N; i++) {
fprintf(out,"%07d \t %.10E \t % .10E % .10E % .10E \t % .10E % .10E % .10E \n",
ind[i],
m[i],
x[i][0], x[i][1], x[i][2],
v[i][0], v[i][1], v[i][2]);
}
fclose(out);
}
void write_bh_data(double time_cur, double m[], double3 x[], double3 v[], double pot[], double3 a[], double3 adot[], double dt[])
{
if (config->live_smbh_count == 2) {
@ -1971,9 +1955,8 @@ int main(int argc, char *argv[])
diskstep++;
char out_fname[256];
sprintf(out_fname, "%06d", diskstep);
if (config->output_hdf5) h5_write(std::string(out_fname) + ".h5", diskstep, N, time_cur, m, x, v, pot, a, adot, 0, true);
else ascii_write(std::string(out_fname) + ".dat", diskstep, N, time_cur, m, x, v, 10);
// TODO custom precision
if (config->output_hdf5) h5_write(std::string(out_fname) + ".h5", diskstep, N, time_cur, m, x, v, pot, a, adot, config->output_extra_mode, config->output_hdf5_double_precision);
else ascii_write(std::string(out_fname) + ".dat", diskstep, N, time_cur, m, x, v, config->output_ascii_precision);
} /* if (myRank == rootRank) */
#ifdef ETICS_DUMP