mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
Slight re-organization of C/C++ tools. Significant modifications to support observational data. Python and pipeline scripts added
This commit is contained in:
P.M. Sutter
parent
15496df4ff
commit
14abbc2018
42 changed files with 16252 additions and 557 deletions
508
c_tools/mock/generateMock.cpp
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508
c_tools/mock/generateMock.cpp
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#include <cmath>
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#include <cassert>
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#include <iostream>
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#include <fstream>
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#include <string>
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#include <CosmoTool/loadSimu.hpp>
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#include <CosmoTool/loadRamses.hpp>
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#include <CosmoTool/loadGadget.hpp>
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#include <CosmoTool/loadFlash.hpp>
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#include <CosmoTool/interpolate.hpp>
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#include <CosmoTool/fortran.hpp>
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#include "generateMock_conf.h"
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#include "gslIntegrate.hpp"
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#include <netcdfcpp.h>
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using namespace std;
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using namespace CosmoTool;
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#define LIGHT_SPEED 299792.458
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SimuData *myLoadGadget(const char *fname, int id, int flags)
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{
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return loadGadgetMulti(fname, id, flags);
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}
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SimuData *doLoadSimulation(const char *gadgetname, int velAxis, bool goRedshift, SimuData *(*loadFunction)(const char *fname, int id, int flags))
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{
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SimuData *d, *outd;
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bool singleFile = false;
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try
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{
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d = loadFunction(gadgetname, -1, 0);
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singleFile = true;
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}
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catch (const NoSuchFileException& e)
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{
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try
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{
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d = loadFunction(gadgetname, 0, 0);
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}
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catch(const NoSuchFileException& e)
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{
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return 0;
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}
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}
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outd = new SimuData;
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outd->NumPart = d->TotalNumPart;
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outd->BoxSize = d->BoxSize/1000;
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outd->TotalNumPart = outd->NumPart;
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outd->Hubble = d->Hubble;
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outd->Omega_Lambda = d->Omega_Lambda;
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outd->Omega_M = d->Omega_M;
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outd->time = d->time;
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for (int k = 0; k < 3; k++)
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outd->Pos[k] = new float[outd->NumPart];
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outd->Vel[2] = new float[outd->NumPart];
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delete d;
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int curCpu = singleFile ? -1 : 0;
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cout << "loading file 0 " << endl;
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try
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{
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while (1)
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{
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d = loadFunction(gadgetname, curCpu, NEED_POSITION|NEED_VELOCITY|NEED_GADGET_ID);
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for (int k = 0; k < 3; k++)
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for (int i = 0; i < d->NumPart; i++)
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{
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assert(d->Id[i] >= 1);
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assert(d->Id[i] <= outd->TotalNumPart);
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outd->Pos[k][d->Id[i]-1] = d->Pos[k][i]/1000;
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outd->Vel[2][d->Id[i]-1] = d->Vel[velAxis][i];
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}
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if (goRedshift)
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for (int i = 0; i < d->NumPart; i++)
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outd->Pos[velAxis][d->Id[i]-1] += d->Vel[velAxis][i]/100.;
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delete d;
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if (singleFile)
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break;
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curCpu++;
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cout << "loading file " << curCpu << endl;
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}
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}
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catch (const NoSuchFileException& e)
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{
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}
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return outd;
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}
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SimuData *doLoadMultidark(const char *multidarkname)
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{
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SimuData *outd;
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FILE *fp;
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int actualNumPart;
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outd = new SimuData;
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cout << "opening multidark file " << multidarkname << endl;
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fp = fopen(multidarkname, "r");
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if (fp == NULL) {
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cout << "could not open file!" << endl;
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return 0;
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}
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fscanf(fp, "%f\n", &outd->BoxSize);
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fscanf(fp, "%f\n", &outd->Omega_M);
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fscanf(fp, "%f\n", &outd->Hubble);
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fscanf(fp, "%f\n", &outd->time);
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fscanf(fp, "%d\n", &outd->NumPart);
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outd->time = 1./(1.+outd->time); // convert to scale factor
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outd->TotalNumPart = outd->NumPart;
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outd->Omega_Lambda = 1.0 - outd->Omega_M;
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for (int k = 0; k < 3; k++)
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outd->Pos[k] = new float[outd->NumPart];
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outd->Vel[2] = new float[outd->NumPart];
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cout << "loading multidark particles" << endl;
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actualNumPart = 0;
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for (int i = 0; i < outd->NumPart; i++) {
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fscanf(fp, "%f %f %f %f\n", &outd->Pos[0][i], &outd->Pos[1][i],
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&outd->Pos[2][i], &outd->Vel[2][i]);
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if (outd->Pos[0][i] == -99 && outd->Pos[1][i] == -99 &&
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outd->Pos[2][i] == -99 && outd->Vel[2][i] == -99) {
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break;
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} else {
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actualNumPart++;
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}
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}
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fclose(fp);
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outd->NumPart = actualNumPart;
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outd->TotalNumPart = actualNumPart;
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return outd;
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}
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static double cubic(double a)
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{
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return a*a*a;
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}
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struct TotalExpansion
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{
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double Omega_M, Omega_L;
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double operator()(double z)
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{
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return 1/sqrt(Omega_M*cubic(1+z) + Omega_L);
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}
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};
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Interpolate make_cosmological_redshift(double OM, double OL, double z0, double z1, int N = 5000)
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{
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TotalExpansion e_computer;
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double D_tilde, Q, Qprime;
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InterpolatePairs pairs;
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e_computer.Omega_M = OM;
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e_computer.Omega_L = OL;
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pairs.resize(N);
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ofstream f("comoving_distance.txt");
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for (int i = 0; i < N; i++)
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{
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double z = z0 + (z1-z0)/N*i;
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pairs[i].second = z;
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pairs[i].first = gslIntegrate(e_computer, 0, z, 1e-3);
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f << z << " " << pairs[i].first << endl;
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}
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return buildFromVector(pairs);
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}
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void metricTransform(SimuData *data, int axis, bool reshift, bool pecvel, double*& expfact)
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{
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int x0, x1, x2;
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switch (axis) {
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case 0:
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x0 = 1; x1 = 2; x2 = 0;
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break;
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case 1:
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x0 = 0; x1 = 2; x2 = 1;
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break;
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case 2:
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x0 = 0; x1 = 1; x2 = 2;
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break;
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default:
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abort();
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}
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double z0 = 1/data->time - 1;
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Interpolate z_vs_D = make_cosmological_redshift(data->Omega_M, data->Omega_Lambda, 0., z0+8*data->BoxSize*100/LIGHT_SPEED); // Redshift 2*z0 should be sufficient ?
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double z_base = reshift ? z0 : 0;
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TotalExpansion e_computer;
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double baseComovingDistance;
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expfact = new double[data->NumPart];
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cout << "Using base redshift z=" << z0 << " " << z0+8*data->BoxSize*100/LIGHT_SPEED << endl;
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e_computer.Omega_M = data->Omega_M;
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e_computer.Omega_L = data->Omega_Lambda;
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baseComovingDistance = LIGHT_SPEED/100.* gslIntegrate(e_computer, 0, z0, 1e-3);
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cout << "Comoving distance = " << baseComovingDistance << " Mpc/h" << endl;
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for (uint32_t i = 0; i < data->NumPart; i++)
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{
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float& x = data->Pos[x0][i];
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float& y = data->Pos[x1][i];
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float& z = data->Pos[x2][i];
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float& v = data->Vel[2][i];
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float z_old = z;
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double reduced_red = (z + baseComovingDistance)*100./LIGHT_SPEED;
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try
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{
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// Distorted redshift
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if (reduced_red == 0)
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z = 0;
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else {
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z = (z_vs_D.compute(reduced_red)-z_base)*LIGHT_SPEED/100.;
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}
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expfact[i] = z / z_old;
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// Add peculiar velocity
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if (pecvel)
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z += v/100;
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}
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catch(const InvalidRangeException& e) {
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cout << "Trying to interpolate out of the tabulated range." << endl;
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cout << "The offending value is z=" << reduced_red << endl;
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abort();
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}
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}
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}
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void generateOutput(SimuData *data, int axis,
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const std::string& fname)
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{
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UnformattedWrite f(fname);
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cout << "Generating output particles to " << fname << endl;
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int x0, x1, x2;
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switch (axis) {
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case 0:
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x0 = 1; x1 = 2; x2 = 0;
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break;
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case 1:
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x0 = 0; x1 = 2; x2 = 1;
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break;
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case 2:
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x0 = 0; x1 = 1; x2 = 2;
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break;
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default:
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abort();
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}
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f.beginCheckpoint();
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f.writeInt32(data->NumPart);
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f.endCheckpoint();
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cout << "Writing X components..." << endl;
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f.beginCheckpoint();
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for (uint32_t i = 0; i < data->NumPart; i++)
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{
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f.writeReal32(data->Pos[x0][i]);
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}
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f.endCheckpoint();
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cout << "Writing Y components..." << endl;
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f.beginCheckpoint();
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for (uint32_t i = 0; i < data->NumPart; i++)
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{
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f.writeReal32(data->Pos[x1][i]);
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}
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f.endCheckpoint();
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cout << "Writing Z components..." << endl;
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f.beginCheckpoint();
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for (uint32_t i = 0; i < data->NumPart; i++)
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{
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f.writeReal32(data->Pos[x2][i]);
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}
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f.endCheckpoint();
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}
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void makeBox(SimuData *simu, double *efac, SimuData *&boxed, generateMock_info& args_info)
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{
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float subsample = args_info.subsample_given ? args_info.subsample_arg : 1.0;
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uint32_t goodParticles = 0;
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double ranges[3][2] = {
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{ args_info.rangeX_min_arg, args_info.rangeX_max_arg },
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{ args_info.rangeY_min_arg, args_info.rangeY_max_arg },
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{ args_info.rangeZ_min_arg, args_info.rangeZ_max_arg }
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};
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double mul[3];
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float minmax[2][3];
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int *particle_id;
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bool *random_acceptance = 0;
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boxed = new SimuData;
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boxed->Hubble = simu->Hubble;
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boxed->Omega_M = simu->Omega_M;
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boxed->Omega_Lambda = simu->Omega_Lambda;
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boxed->time = simu->time;
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boxed->BoxSize = simu->BoxSize;
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random_acceptance = new bool[simu->NumPart];
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for (int j = 0; j < 3; j++) minmax[1][j] = minmax[0][j] = simu->Pos[j][0];
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for (uint32_t i = 0; i < simu->NumPart; i++)
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{
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bool acceptance = true;
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for (int j = 0; j < 3; j++) {
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acceptance =
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acceptance &&
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(simu->Pos[j][i] > ranges[j][0]) &&
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(simu->Pos[j][i] < ranges[j][1]);
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minmax[0][j] = min(simu->Pos[j][i], minmax[0][j]);
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minmax[1][j] = max(simu->Pos[j][i], minmax[1][j]);
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}
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random_acceptance[i] = acceptance && (drand48() <= subsample);
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if (random_acceptance[i])
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goodParticles++;
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}
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cout << "Subsample fraction: " << subsample << endl;
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cout << "Min range = " << ranges[0][0] << " " << ranges[1][0] << " " << ranges[2][0] << endl;
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cout << "Max range = " << ranges[0][1] << " " << ranges[1][1] << " " << ranges[2][1] << endl;
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cout << "Min position = " << minmax[0][0] << " " << minmax[0][1] << " " << minmax[0][2] << endl;
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cout << "Max position = " << minmax[1][0] << " " << minmax[1][1] << " " << minmax[1][2] << endl;
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cout << "Number of accepted particles: " << goodParticles << endl;
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for (int j = 0; j < 3; j++)
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{
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boxed->Pos[j] = new float[goodParticles];
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boxed->Vel[j] = 0;
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mul[j] = 1.0/(ranges[j][1] - ranges[j][0]);
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}
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cout << "Rescaling factors = " << mul[0] << " " << mul[1] << " " << mul[2] << endl;
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boxed->NumPart = goodParticles;
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particle_id = new int[goodParticles];
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double *expansion_fac = new double[goodParticles];
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uint32_t k = 0;
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for (uint32_t i = 0; i < simu->NumPart; i++)
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{
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bool acceptance = random_acceptance[i];
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if (acceptance)
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{
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for (int j = 0; j < 3; j++)
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{
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boxed->Pos[j][k] = (simu->Pos[j][i]-ranges[j][0])*mul[j];
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assert(boxed->Pos[j][k] > 0);
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assert(boxed->Pos[j][k] < 1);
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}
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particle_id[k] = i;
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expansion_fac[k] = efac[i];
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k++;
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}
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}
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delete[] random_acceptance;
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NcFile f(args_info.outputParameter_arg, NcFile::Replace);
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f.add_att("range_x_min", ranges[0][0]);
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f.add_att("range_x_max", ranges[0][1]);
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f.add_att("range_y_min", ranges[1][0]);
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f.add_att("range_y_max", ranges[1][1]);
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f.add_att("range_z_min", ranges[2][0]);
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f.add_att("range_z_max", ranges[2][1]);
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NcDim *NumPart_dim = f.add_dim("numpart_dim", boxed->NumPart);
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NcVar *v = f.add_var("particle_ids", ncInt, NumPart_dim);
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NcVar *v2 = f.add_var("expansion", ncDouble, NumPart_dim);
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v->put(particle_id, boxed->NumPart);
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v2->put(expansion_fac, boxed->NumPart);
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delete[] particle_id;
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delete[] expansion_fac;
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}
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int main(int argc, char **argv)
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{
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generateMock_info args_info;
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generateMock_conf_params args_params;
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SimuData *simu, *simuOut;
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generateMock_conf_init(&args_info);
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generateMock_conf_params_init(&args_params);
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args_params.check_required = 0;
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if (generateMock_conf_ext (argc, argv, &args_info, &args_params))
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return 1;
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if (!args_info.configFile_given)
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{
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if (generateMock_conf_required (&args_info, GENERATEMOCK_CONF_PACKAGE))
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return 1;
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}
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else
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{
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args_params.check_required = 1;
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args_params.initialize = 0;
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if (generateMock_conf_config_file (args_info.configFile_arg,
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&args_info,
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&args_params))
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return 1;
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}
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generateMock_conf_print_version();
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if (args_info.ramsesBase_given || args_info.ramsesId_given)
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{
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if (args_info.ramsesBase_given && args_info.ramsesId_given) {
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//simu = doLoadRamses(args_info.ramsesBase_arg,
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// args_info.ramsesId_arg,
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// args_info.axis_arg, false);
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}
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else
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{
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cerr << "Both ramsesBase and ramsesId are required to be able to load snapshots" << endl;
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return 1;
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}
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if (simu == 0)
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{
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cerr << "Error while loading" << endl;
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return 1;
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}
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}
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else if (args_info.gadget_given || args_info.flash_given || args_info.multidark_given)
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{
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if (args_info.gadget_given && args_info.flash_given)
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{
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cerr << "Do not know which file to use: Gadget or Flash ?" << endl;
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return 1;
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}
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if (args_info.multidark_given) {
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simu = doLoadMultidark(args_info.multidark_arg);
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||||
}
|
||||
|
||||
if (args_info.gadget_given) {
|
||||
simu = doLoadSimulation(args_info.gadget_arg, args_info.axis_arg, false, myLoadGadget);
|
||||
}
|
||||
if (args_info.flash_given) {
|
||||
simu = doLoadSimulation(args_info.flash_arg, args_info.axis_arg, false, loadFlashMulti);
|
||||
}
|
||||
|
||||
if (simu == 0)
|
||||
{
|
||||
cerr << "Error while loading " << endl;
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
cerr << "Either a ramses snapshot or a gadget snapshot is required." << endl;
|
||||
return 1;
|
||||
}
|
||||
cout << "Hubble = " << simu->Hubble << endl;
|
||||
cout << "Boxsize = " << simu->BoxSize << endl;
|
||||
cout << "Omega_M = " << simu->Omega_M << endl;
|
||||
cout << "Omega_Lambda = " << simu->Omega_Lambda << endl;
|
||||
|
||||
double *expfact;
|
||||
|
||||
if (args_info.cosmo_flag){
|
||||
metricTransform(simu, args_info.axis_arg, args_info.preReShift_flag, args_info.peculiarVelocities_flag, expfact);
|
||||
} else {
|
||||
expfact = new double[simu->NumPart];
|
||||
for (int j = 0; j < simu->NumPart; j++) expfact[j] = 1.0;
|
||||
}
|
||||
|
||||
makeBox(simu, expfact, simuOut, args_info);
|
||||
delete simu;
|
||||
|
||||
generateOutput(simuOut, args_info.axis_arg, args_info.output_arg);
|
||||
|
||||
delete simuOut;
|
||||
|
||||
printf("Done!\n");
|
||||
return 0;
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue