Make TAUTAIL, the stopping criterion for optical depth profiles, conf…

…igurable

TAUTAIL gives the minimum optical depth each particle can
contribute to a pixel (although the nearest pixel is always included).
Make this runtime configurable instead of a compile constant.

cextract/main.cpp

@@ -184,7 +184,7 @@ int main(int argc, char **argv)
     populate_los_table(cofm, axis,NumLos, ext_table, box100);
     /*Setup the interpolator*/
     const double velfac = atime/h100*Hz/1e3;
-    ParticleInterp pint(NBINS, LAMBDA_LYA_H1, GAMMA_LYA_H1, FOSC_LYA, HMASS, box100, velfac, atime, cofm, axis,NumLos,1);
+    ParticleInterp pint(NBINS, LAMBDA_LYA_H1, GAMMA_LYA_H1, FOSC_LYA, HMASS, box100, velfac, atime, cofm, axis,NumLos,1, 1e-5);
   if(!(output=fopen(outname.c_str(),"w")))
   {
           fprintf(stderr, "Error opening %s: %s\n",outname.c_str(), strerror(errno));

fake_spectra/absorption.cpp

@@ -32,10 +32,6 @@
 /*Conversion factor between internal energy and mu and temperature in K */
 #define TSCALE ((GAMMA-1.0) * PROTONMASS * ESCALE / BOLTZMANN)
 
-//Threshold of tau below which we stop computing profiles
-//Note that because this is for each particle, it should be fairly small.
-#define TAUTAIL 1e-5
-
 /* Find the integral of the particle density in this pixel by integrating an SPH kernel
  * over the z direction.
  * Arguments:
@@ -105,7 +101,8 @@ kern_frac_func get_kern_frac(const int kernel)
 
 //Factor of 1e5 in bfac converts from cm/s to km/s
 //Factor of 1e5 in voigt_fac converts from cm/s to km/s
-LineAbsorption::LineAbsorption(const double lambda, const double gamma, const double fosc, const double amumass, const double velfac_i, const double boxsize, const double atime_i,const int kernel_i):
+LineAbsorption::LineAbsorption(const double lambda, const double gamma, const double fosc, const double amumass, const double velfac_i, const double boxsize, const double atime_i,const int kernel_i, const double tautail):
+tautail(tautail),
 sigma_a( sqrt(3.0*M_PI*SIGMA_T/8.0) * lambda  * fosc ),
 bfac( sqrt(2.0*BOLTZMANN/(amumass*PROTONMASS))/1e5 ),
 voigt_fac( gamma*lambda/(4.*M_PI)/1e5 ),
@@ -187,7 +184,7 @@ void LineAbsorption::add_tau_particle(double * tau, const int nbins, const doubl
         j+=nbins;
       tau[j]+=taulast;
       //Absorption will only decrease as you go further from the particle.
-      if(taulast < TAUTAIL)
+      if(taulast < tautail)
         break;
   }
   //Go from the particle backwards
@@ -201,7 +198,7 @@ void LineAbsorption::add_tau_particle(double * tau, const int nbins, const doubl
         j+=nbins;
       tau[j]+=taulast;
       //Absorption will only decrease as you go further from the particle.
-      if(taulast < TAUTAIL)
+      if(taulast < tautail)
         break;
   }
 }

fake_spectra/absorption.h

@@ -26,7 +26,7 @@ class LineAbsorption
          * gamma: transition rate in 1/s
          * fosc: oscillation fraction
          * */
-        LineAbsorption(const double lambda, const double gamma, const double fosc, const double amumass, const double velfac_i, const double boxsize, const double atime_i, const int kernel_i);
+        LineAbsorption(const double lambda, const double gamma, const double fosc, const double amumass, const double velfac_i, const double boxsize, const double atime_i, const int kernel_i, const double tautail);
 
         /* Add the absorption from a particle to the spectrum in the array
          * tau, or the density from the particle to the array colden,
@@ -52,6 +52,9 @@ class LineAbsorption
         void add_tau_particle(double * tau, const int nbins, const double dr2, const float dens, const float ppos, const float pvel, const float temp, const float smooth);
 
     private:
+        /* Threshold of tau below which we stop computing profiles.
+         * Note that because this is for each particle, it should be fairly small.*/
+        const double tautail;
         /* Absorption cross-sections cm^2 */
         const double sigma_a;
         /* Constant factor to turn sqrt(temperature) in K into velocity in km/s*/

fake_spectra/part_int.h

@@ -24,8 +24,8 @@
 class ParticleInterp: public LineAbsorption
 {
     public:
-        ParticleInterp(const int nbins_i, const double lambda, const double gamma, const double fosc, const double amumass, const double boxsize, const double velfac, const double atime, const double cofm[], const int axis[], const int NumLos, const int kernel):
-        LineAbsorption(lambda, gamma, fosc, amumass, velfac, boxsize, atime, kernel),
+        ParticleInterp(const int nbins_i, const double lambda, const double gamma, const double fosc, const double amumass, const double boxsize, const double velfac, const double atime, const double cofm[], const int axis[], const int NumLos, const int kernel, const double tautail):
+        LineAbsorption(lambda, gamma, fosc, amumass, velfac, boxsize, atime, kernel, tautail),
         nbins(nbins_i),nlos(NumLos),
         sort_los_table(cofm, axis, NumLos, boxsize)
         {

fake_spectra/py_module.cpp

@@ -104,16 +104,16 @@ extern "C" PyObject * Py_Particle_Interpolation(PyObject *self, PyObject *args)
     //Things which should be from input
     int nbins, NumLos, compute_tau, kernel;
     long long Npart;
-    double box100, velfac, lambda, gamma, fosc, amumass, atime;
+    double box100, velfac, lambda, gamma, fosc, amumass, atime, tautail;
     npy_intp size[2];
     //Input variables in np format
     PyArrayObject *pos, *vel, *dens, *temp, *h;
     PyArrayObject *cofm, *axis;
 
     //Get our input
-    if(!PyArg_ParseTuple(args, "iiidddddddO!O!O!O!O!O!O!", &compute_tau, &nbins, &kernel, &box100,  &velfac, &atime, &lambda, &gamma, &fosc, &amumass, &PyArray_Type, &pos, &PyArray_Type, &vel, &PyArray_Type, &dens, &PyArray_Type, &temp, &PyArray_Type, &h, &PyArray_Type, &axis, &PyArray_Type, &cofm) )
+    if(!PyArg_ParseTuple(args, "iiiddddddddO!O!O!O!O!O!O!", &compute_tau, &nbins, &kernel, &box100,  &velfac, &atime, &lambda, &gamma, &fosc, &amumass, &tautail, &PyArray_Type, &pos, &PyArray_Type, &vel, &PyArray_Type, &dens, &PyArray_Type, &temp, &PyArray_Type, &h, &PyArray_Type, &axis, &PyArray_Type, &cofm) )
     {
-      PyErr_SetString(PyExc_AttributeError, "Incorrect arguments: use compute_tau, nbins, boxsize, velfac, atime, lambda, gamma, fosc, species mass (amu), pos, vel, dens, temp, h, axis, cofm\n");
+      PyErr_SetString(PyExc_AttributeError, "Incorrect arguments: use compute_tau, nbins, boxsize, velfac, atime, lambda, gamma, fosc, species mass (amu), min. tau,  pos, vel, dens, temp, h, axis, cofm\n");
       return NULL;
     }
 
@@ -167,7 +167,7 @@ extern "C" PyObject * Py_Particle_Interpolation(PyObject *self, PyObject *args)
         PyErr_SetString(PyExc_MemoryError, "Getting contiguous copies of input arrays failed\n");
         return NULL;
     }
-    ParticleInterp pint(nbins, lambda, gamma, fosc, amumass, box100, velfac, atime, Cofm, Axis ,NumLos, kernel);
+    ParticleInterp pint(nbins, lambda, gamma, fosc, amumass, box100, velfac, atime, Cofm, Axis ,NumLos, kernel, tautail);
 
     PyObject * for_return;
     /* Allocate array space. This is (I hope) contiguous.

fake_spectra/spectra.py

@@ -104,6 +104,9 @@ def __init__(self,num, base,cofm, axis, res=1., cdir=None, savefile="spectra.hdf
         self.cdir = cdir
         #Minimum length of spectra within which to look at metal absorption (in km/s)
         self.minwidth = 500.
+        #Stopping criterion for optical depth: if a particle is adding less
+        #than this to a pixel, stop the integration.
+        self.tautail = 1e-5
         try:
             if load_snapshot:
                 self.snapshot_set = absn.AbstractSnapshotFactory(num, base)
@@ -505,7 +508,7 @@ def _get_elem_den(self, elem, ion, den, temp, ind, ind2):
     def _do_interpolation_work(self,pos, vel, elem_den, temp, hh, amumass, line, get_tau):
         """Run the interpolation on some pre-determined arrays, spat out by _read_particle_data"""
         #Factor of 10^-8 converts line width (lambda_X) from Angstrom to cm
-        return _Particle_Interpolate(get_tau*1, self.nbins, self.snapshot_set.get_kernel(), self.box, self.velfac, self.atime, line.lambda_X*1e-8, line.gamma_X, line.fosc_X, amumass, pos, vel, elem_den, temp, hh, self.axis, self.cofm)
+        return _Particle_Interpolate(get_tau*1, self.nbins, self.snapshot_set.get_kernel(), self.box, self.velfac, self.atime, line.lambda_X*1e-8, line.gamma_X, line.fosc_X, amumass, self.tautail, pos, vel, elem_den, temp, hh, self.axis, self.cofm)
 
     def particles_near_lines(self, pos, hh,axis=None, cofm=None):
         """Filter a particle list, returning an index list of those near sightlines"""