Commit 893398bc authored by Christopher Subich's avatar Christopher Subich
Browse files

Merge branch 'refactor-QSP' into 'master'

Refactor qsp

See merge request !15
parents 6e22524e d220e07a
......@@ -253,14 +253,38 @@ void compute_lambda2(TArrayn::DTArray & lambda2, TArrayn::DTArray & u,
/* Creates and outputs data for plotting a bivariate histogram with NS*NT bins
* between tracers S1 and T1 to "filename.csv" (don't include file extension).
*/
void QSPCount(const TArrayn::DTArray &t, const TArrayn::DTArray &u,
const TArrayn::DTArray &v, const TArrayn::DTArray &w,
const char T1_name, const char S1_name, const int NS,
const int NT, double T1_max, double S1_max, double T1_min,
double S1_min, const int Nx, const int Ny, const int Nz,
string filename, const int plotnum, bool mapped,
TArrayn::DTArray *xgrid, TArrayn::DTArray *ygrid,
TArrayn::DTArray *zgrid);
struct QSPOptions {
int NS;
int NT;
string filename;
double S1_max;
double S1_min;
double T1_max;
double T1_min;
string T1_name;
string S1_name;
};
struct QSPData {
TArrayn::DTArray *u;
TArrayn::DTArray *v;
TArrayn::DTArray *w;
TArrayn::DTArray *temp;
TArrayn::DTArray *rho;
TArrayn::DTArray *salinity;
TArrayn::DTArray *custom_T1;
TArrayn::DTArray *custom_S1;
TArrayn::DTArray *xgrid;
TArrayn::DTArray *ygrid;
TArrayn::DTArray *zgrid;
int Nx;
int Ny;
int Nz;
int plotnum;
bool mapped;
};
void QSPCount(QSPOptions qsp_options, QSPData qsp_data);
// Equation of state for seawater, polynomial fit from
// Brydon, Sun, Bleck (1999) (JGR)
......
This diff is collapsed.
......@@ -36,7 +36,7 @@ const int z_ind = 2;
// QSP variables
double T1_max, S1_max, T1_min, S1_min;
char T1_name, S1_name;
string T1_name, S1_name;
int NT, NS;
string QSP_filename;
bool use_salinity;
......@@ -152,7 +152,7 @@ class userControl : public BaseCase {
zgrid = NULL;
}
if ( do_enst_stretch ) temp3 = alloc_array(Nx,Ny,Nz);
if ( do_enst_stretch or do_hist ) temp3 = alloc_array(Nx,Ny,Nz);
}
if ( do_barvor ) {
......@@ -430,13 +430,6 @@ class userControl : public BaseCase {
// nor to make deep copies of them
if ( do_hist ){
if (use_salinity) {
init_tracer_restart("s", *temp1);
} else if (T1_name == 't' || S1_name == 't' || T1_name == 'T' ||
S1_name == 'T') {
init_tracer_restart("t", *temp1);
}
// If user asked to grab the grids, we populate the grids
// with the correct data from disk
if (mapped) {
......@@ -449,9 +442,49 @@ class userControl : public BaseCase {
assert(zgrid == NULL);
}
QSPCount(*temp1, u, v, w, T1_name, S1_name, NS, NT, T1_max,
S1_max, T1_min, S1_min, Nx, Ny, Nz, QSP_filename,
plotnum, mapped, xgrid, ygrid, zgrid);
QSPOptions qsp_opts;
qsp_opts.S1_name = S1_name;
qsp_opts.T1_name = T1_name;
qsp_opts.filename = QSP_filename;
qsp_opts.NS = NS;
qsp_opts.NT = NT;
qsp_opts.S1_max = S1_max;
qsp_opts.S1_min = S1_min;
qsp_opts.T1_max = T1_max;
qsp_opts.T1_min = T1_min;
QSPData qsp_data;
qsp_data.mapped = mapped;
qsp_data.Nx = Nx;
qsp_data.Ny = Ny;
qsp_data.Nz = Nz;
qsp_data.plotnum = plotnum;
qsp_data.u = &u;
qsp_data.v = &v;
qsp_data.w = &w;
qsp_data.xgrid = xgrid;
qsp_data.ygrid = ygrid;
qsp_data.zgrid = zgrid;
qsp_data.temp = NULL;
qsp_data.rho = NULL;
qsp_data.salinity = NULL;
if (use_salinity) {
init_tracer_restart("s", *temp1);
qsp_data.salinity = temp1;
}
if (T1_name.compare("temp") == 0 || S1_name.compare("temp") == 0) {
init_tracer_restart("t", *temp2);
qsp_data.temp = temp2;
}
if (T1_name.compare("rho") == 0 || S1_name.compare("rho") == 0) {
init_tracer_restart("rho", *temp3);
qsp_data.rho = temp3;
}
QSPCount(qsp_opts, qsp_data);
if (master()) {
fprintf(stdout, "Completed the write for QSP.%d\n", plotnum);
}
......@@ -530,13 +563,13 @@ int main(int argc, char ** argv) {
add_option("do_Q_and_R",&do_Q_and_R,false,"Calculate Q and R?");
add_option("do_lambda2",&do_lambda2,false,"Calculate Lambda2?");
add_option("do_hist",&do_hist,false,"Create QSP Data?");
add_option("T1",&T1_name,'t', "Name of tracer 1 for QSP. Valid values are t (for rho),u,v,w,T (for temp) or k for K.E.");
add_option("S1",&S1_name,'w', "Name of tracer 2 for QSP. Valid values are t (for rho),u,v,w,T (for temp) or k for K.E.");
add_option("T1",&T1_name,"u", "Name of tracer 1 for QSP. Valid values are rho,u,v,w,temp or ke");
add_option("S1",&S1_name,"w", "Name of tracer 2 for QSP. Valid values are rho,u,v,w,temp or ke");
add_option("T1_max",&T1_max,std::numeric_limits<double>::max(), "Maximum explicit bin for T1 in QSP.");
add_option("T1_min",&T1_min,std::numeric_limits<double>::min(), "Minimum explicit bin for T1 in QSP.");
add_option("S1_max",&S1_max,std::numeric_limits<double>::max(), "Maximum explicit bin for S1 in QSP.");
add_option("S1_min",&S1_min,std::numeric_limits<double>::min(), "Minimum explicit bin for S1 in QSP.");
add_option("QSP_salinity",&use_salinity, false, "Should salinity be read in from filename s?.");
add_option("salinity",&use_salinity, false, "Should salinity be read in from filename s?.");
add_option("QSP_filename",&QSP_filename,"QSP_default", "Filename to save data to. Don't include file extension.");
add_option("NS",&NS,10,"Number of bins for tracer S");
add_option("NT",&NT,10,"Number of bins for tracer T");
......
......@@ -42,11 +42,11 @@ do_Q = false
do_R = false
do_Q_and_R = false
do_lambda2 = false
do_hist = false
# QSP Parameters
T1 = t
S1 = k
do_hist = false
T1 = temp
S1 = ke
QSP_filename = QSP
NT = 10
NS = 10
/* Derivative case file for computing derivatives of existing fields */
// only able to return first and second derivatives
/* ------------------ Top matter --------------------- */
// Required headers
#include "../../BaseCase.hpp" // contains default class
#include "../../Options.hpp" // config-file parser
#include "../../Science.hpp" // Science content
#include <cassert>
#include <limits>
#include <string>
// Tensor variables for indexing
blitz::firstIndex ii;
blitz::secondIndex jj;
blitz::thirdIndex kk;
/* ------------------ Define parameters --------------------- */
// Grid scales
double Lx, Ly, Lz; // Grid lengths (m)
int Nx, Ny, Nz; // Number of points in x, y, z
// Mapped grid?
bool mapped;
// Grid types
DIMTYPE intype_x, intype_y, intype_z;
string grid_type[3];
// Expansion types and indices
S_EXP expan[3];
const int x_ind = 0;
const int y_ind = 1;
const int z_ind = 2;
// QSP variables
double T1_max, S1_max, T1_min, S1_min;
std::string T1_name, S1_name;
int NT, NS;
std::string QSP_filename;
bool use_salinity, read_rho;
std::string salinity_filename, temp_filename, rho_filename;
std::string custom_T1_filename, custom_S1_filename;
const double double_max = std::numeric_limits<double>::max();
// current output number
int plotnum;
// Derivative options
int start_sequence; // output number to start taking derivatives at
int final_sequence; // output number to stop taking derivatives at
int step_sequence; // step between outputs to take derivatives
// streching/tilting?
bool v_exist; // Does the v field exist?
/* ------------------ Adjust the class --------------------- */
class userControl : public BaseCase {
public:
/* Initialize things */
DTArray *xgrid, *ygrid, *zgrid; // Arrays for storing grid data
/* Size of domain */
double length_x() const { return Lx; }
double length_y() const { return Ly; }
double length_z() const { return Lz; }
/* Resolution in X, Y, and Z */
int size_x() const { return Nx; }
int size_y() const { return Ny; }
int size_z() const { return Nz; }
/* Set expansions (FREE_SLIP, NO_SLIP (in vertical) or PERIODIC) */
DIMTYPE type_x() const { return intype_x; }
DIMTYPE type_y() const { return intype_y; }
DIMTYPE type_z() const { return intype_z; }
/* Set other things */
int get_restart_sequence() const { return plotnum; }
/* Read grid (if mapped) */
bool is_mapped() const { return mapped; }
void do_mapping(DTArray &xg, DTArray &yg, DTArray &zg) {
init_grid_restart("x", "xgrid", xg);
if (Ny > 1)
init_grid_restart("y", "ygrid", yg);
init_grid_restart("z", "zgrid", zg);
}
/* Read fields and do derivatives */
void init_vels(DTArray &u, DTArray &v, DTArray &w) {
// If user asks to grab the grids, we allocate arrays to store
// them in memory
if (mapped) {
xgrid = alloc_array(Nx, Ny, Nz);
if (Ny > 1) {
ygrid = alloc_array(Nx, Ny, Nz);
}
zgrid = alloc_array(Nx, Ny, Nz);
do_mapping(*xgrid, *ygrid, *zgrid);
} else {
// If user doesn't want to grab grids, we make sure not to
// allocate arrays for them and to set the pointers to NULL.
xgrid = NULL;
ygrid = NULL;
zgrid = NULL;
}
QSPOptions qsp_opts;
qsp_opts.S1_name = S1_name;
qsp_opts.T1_name = T1_name;
qsp_opts.filename = QSP_filename;
qsp_opts.NS = NS;
qsp_opts.NT = NT;
qsp_opts.S1_max = S1_max;
qsp_opts.S1_min = S1_min;
qsp_opts.T1_max = T1_max;
qsp_opts.T1_min = T1_min;
QSPData qsp_data;
qsp_data.mapped = mapped;
qsp_data.Nx = Nx;
qsp_data.Ny = Ny;
qsp_data.Nz = Nz;
qsp_data.xgrid = xgrid;
qsp_data.ygrid = ygrid;
qsp_data.zgrid = zgrid;
// Compute derivatives at each requested output
for (plotnum = start_sequence; plotnum <= final_sequence;
plotnum = plotnum + step_sequence) {
// read in fields (if not already stored in memory)
// Compute QSP data. The code promises to not mutate the arrays,
// nor to make deep copies of them
// u
init_tracer_restart("u", u);
// v
if (v_exist) {
init_tracer_restart("v", v);
} else {
if (master())
fprintf(stdout, "No v field, setting v=0\n");
v = 0;
}
// w
init_tracer_restart("w", w);
qsp_data.plotnum = plotnum;
qsp_data.u = &u;
qsp_data.v = &v;
qsp_data.w = &w;
qsp_data.temp = NULL;
qsp_data.rho = NULL;
qsp_data.salinity = NULL;
qsp_data.custom_T1 = NULL;
qsp_data.custom_S1 = NULL;
DTArray *arr_salinity, *arr_temperature, *arr_rho, *custom_T1, *custom_S1;
if (use_salinity) {
arr_salinity = alloc_array(Nx, Ny, Nz);
init_tracer_restart(salinity_filename, *arr_salinity);
qsp_data.salinity = arr_salinity;
}
if (read_rho) {
arr_rho = alloc_array(Nx, Ny, Nz);
init_tracer_restart(rho_filename, *arr_rho);
qsp_data.rho = arr_rho;
}
if (T1_name.compare("temp") == 0 || S1_name.compare("temp") == 0) {
arr_temperature = alloc_array(Nx, Ny, Nz);
init_tracer_restart(temp_filename, *arr_temperature);
qsp_data.temp = arr_temperature;
}
if (T1_name.compare("custom") == 0) {
custom_T1 = alloc_array(Nx, Ny, Nz);
init_tracer_restart(custom_T1_filename, *custom_T1);
qsp_data.custom_T1 = custom_T1;
}
if (S1_name.compare("custom") == 0) {
custom_S1 = alloc_array(Nx, Ny, Nz);
init_tracer_restart(custom_S1_filename, *custom_S1);
qsp_data.custom_S1 = custom_S1;
}
QSPCount(qsp_opts, qsp_data);
if (master()) {
fprintf(stdout, "Completed QSP calculation for plotnum %d\n", plotnum);
}
}
}
// Constructor: Initialize local variables
userControl() {
compute_quadweights(size_x(), size_y(), size_z(), length_x(), length_y(),
length_z(), type_x(), type_y(), type_z());
}
};
/* The ''main'' routine */
int main(int argc, char **argv) {
/* Initialize MPI. This is required even for single-processor runs,
since the inner routines assume some degree of parallelization,
even if it is trivial. */
MPI_Init(&argc, &argv);
/* ------------------ Define parameters from spins.conf ---------------------
*/
options_init();
option_category("Grid Options");
add_option("Lx", &Lx, "Length of tank");
add_option("Ly", &Ly, 1.0, "Width of tank");
add_option("Lz", &Lz, "Height of tank");
add_option("Nx", &Nx, "Number of points in X");
add_option("Ny", &Ny, 1, "Number of points in Y");
add_option("Nz", &Nz, "Number of points in Z");
option_category("Grid mapping options");
add_option("mapped_grid", &mapped, false, "Is the grid mapped?");
string xgrid_type, ygrid_type, zgrid_type;
add_option("type_x", &xgrid_type,
"Grid type in X. Valid values are:\n"
" FOURIER: Periodic\n"
" FREE_SLIP: Cosine expansion\n"
" NO_SLIP: Chebyhsev expansion");
add_option("type_y", &ygrid_type, "FOURIER", "Grid type in Y");
add_option("type_z", &zgrid_type, "Grid type in Z");
option_category("QSP options");
add_option("start_sequence", &start_sequence,
"Sequence number to start taking derivatives at");
add_option("final_sequence", &final_sequence,
"Sequence number to stop taking derivatives at");
add_option("step_sequence", &step_sequence, 1,
"Step between outputs to take derivatives");
add_option("salinity_filename", &salinity_filename,
"Base Filename of Salinity data (optional).");
add_option("temp_filename", &temp_filename,
"Base Filename of temperature data (optional).");
add_option("T1_filename", &custom_T1_filename,
"Base Filename of custom tracer for T1.");
add_option("S1_filename", &custom_S1_filename,
"Base Filename of custom tracer for S1.");
add_option("T1", &T1_name, "u",
"Name of tracer 1 for QSP. Valid values are rho,u,v,w,temp, "
"salinity or ke");
add_option("S1", &S1_name, "w",
"Name of tracer 2 for QSP. Valid values are rho,u,v,w,temp, "
"salinity or ke");
add_option("T1_max", &T1_max, double_max,
"Maximum explicit bin for T1 in QSP.");
add_option("T1_min", &T1_min, -double_max,
"Minimum explicit bin for T1 in QSP.");
add_option("S1_max", &S1_max, double_max,
"Maximum explicit bin for S1 in QSP.");
add_option("S1_min", &S1_min, -double_max,
"Minimum explicit bin for S1 in QSP.");
add_option("salinity", &use_salinity, false,
"Should salinity be read in from a file?.");
add_option("read_rho", &read_rho, false,
"Should rho be read in from a file?.");
add_option("QSP_filename", &QSP_filename, "QSP_default",
"Filename to save data to. Don't include file extension.");
add_option("NS", &NS, 10, "Number of bins for tracer S");
add_option("NT", &NT, 10, "Number of bins for tracer T");
add_option("v_exist", &v_exist, "Does the v field exist?");
// Parse the options from the command line and config file
options_parse(argc, argv);
/* ------------------ Adjust and check parameters --------------------- */
/* Now, make sense of the options received. Many of these values
can be directly used, but the ones of string-type need further procesing.
*/
// parse expansion types
parse_boundary_conditions(xgrid_type, ygrid_type, zgrid_type, intype_x,
intype_y, intype_z);
// vector of string types
grid_type[x_ind] = xgrid_type;
grid_type[y_ind] = ygrid_type;
grid_type[z_ind] = zgrid_type;
// adjust Ly for 2D
if (Ny == 1 and Ly != 1.0) {
Ly = 1.0;
if (master())
fprintf(stdout, "Simulation is 2 dimensional, "
"Ly has been changed to 1.0 for normalization.\n");
}
/* ------------------ Do stuff --------------------- */
userControl mycode; // Create an instantiated object of the above class
FluidEvolve<userControl> kevin_kh(&mycode);
kevin_kh.initialize();
MPI_Finalize();
return 0;
}
## QSP configuration file
# Spatial Parameters
Lx = 6.4
Ly = 1.0
Lz = 0.3
Nx = 4096
Ny = 1
Nz = 384
# Expansion types
type_x = FREE_SLIP
type_y = FOURIER
type_z = NO_SLIP
mapped_grid = false
v_exist = false
# If salinity is needed (directly or indirectly) set this to true
salinity = false
salinity_filename = s
# If you already pre-computed rho (the equation of state) and saved it to a
# file, then set this to true. If this is false, and QSP can find the
# temperature data but not rho, it will use the equation of state function from
# Science.hpp, and if it also finds salinity it will add that to the equation
# of state calculation too.
read_rho = false
rho_filename = rho
# Sequence Options
start_sequence = 0
final_sequence = 0
step_sequence = 1
# Choose what tracers you want to use. T1 and S1 have no distinguishable
# meaning, just stay consistent with NT and NS. Do note that if you pick ke
# then QSP will compute it in-place. If you already pre-computed ke and have a
# saved file for it, use the custom property explained below instead.
# Tracer options: rho, temp, salinity, u, v, w, ke
#
# Note: If you need to use a custom tracer (i.e. not one of the above), set the
# tracer name to "custom." If you do this however, it is your responsability to
# ensure that:
# a) you provide a valid custom filename too and
# b) all prepocessing is already completed and the data in the file is exactly
# what you want to use
T1 = temp
S1 = ke
# Tracer base filenames. These are only relevent parameters IFF you set the
# according tracer name to "custom" above. Otherwise, these are ignored.
T1_filename = vorticity
S1_filename = vorticity
# Set the min/max values of the first/last bin in each dimension respectively.
# These are optional parameters. If you remove these lines from the config QSP
# will find the global min/max values for each timestep and use that instead.
# So if you need fixed values for these make sure to include them!
T1_min = 1
T1_max = 1
S1_min = 1
S1_max = 1
# Number of bins for T1 and S1 chosen above.
NT = 10
NS = 10
# Base filename to save results
QSP_filename = QSP
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