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‎.travis.yml

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language: c
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sudo: required
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before_install:
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- sudo apt-get install gfortran
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matrix:
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include:
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- os: linux
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dist: trusty
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sudo: required
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env: PLUMED_CC=mpif90 PLUMED_CXX=mpif90 MAKEDOC=yes PLUMED_ALL_TESTS=yes
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- os: linux
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dist: trusty
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sudo: required
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env: PLUMED_CC=mpif90 PLUMED_CXX=mpif90 PLUMED_CXXFLAGS=-O3 LAPACK=yes CONFIG_FLAGS="--disable-external-lapack"
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install:
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update -qq ; fi
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- if test "$PLUMED_CXX" == "mpif90" -a "$TRAVIS_OS_NAME" == "linux" ; then sudo apt-get install -y libopenmpi-dev openmpi-bin ; fi
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- make
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script:
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- if test "$PLUMED_CXX" ; then make; fi

‎README.md

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# MOCASSIN-3.0
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MOnte CArlo SimulationS of Ionized Nebulae, Version 3.0
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## MOCASSIN-3.0
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[![Build Status](https://travis-ci.org/equib/MOCASSIN-3.0.svg?branch=master)](https://travis-ci.org/equib/MOCASSIN-3.0)
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[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/equib/mocassin-3.0)
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**MOnte CArlo SimulationS of Ionized Nebulae**, Version 3.0
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Copyright (C) 2007 Barbara Ercolano
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### Installation
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How to compile:
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make mocassin
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make mocassinWarm
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make mocassinOutput
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make mocassinPlot
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How to clean:
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make clean
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How to run:
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mpirun -np N ./mocassin
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where N is number of processors for parallel computing.
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### References
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* Ercolano, B., Clarke, C. J., & Drake, J. J., [ApJ, 699, 1639, 2009](http://adsabs.harvard.edu/abs/2009ApJ...699.1639E)
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* Ercolano, B., Drake, J. J., Raymond, J. C., & Clarke, C. C., [ApJ, 688, 398-407, 2008](http://adsabs.harvard.edu/abs/2008ApJ...688..398E)

‎accessories/dustShellInput.in

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4.48e15 8.51e17 ! rin, rout
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0.005 ! mdmg
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'mrnsizes.dat' ! sizefile
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'mrnspecies.dat'! speciesfile
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50 50 50 ! nx ny nz

‎accessories/makeClothoShell.f90

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program makeDustShell
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implicit none
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real(kind = 8) :: rin, rout, radius, normWeight
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real(kind = 8) :: dx, dy, dz, den, dx1
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real(kind = 8) :: mdmg, sums, Pi = 3.1416
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real(kind = 8), pointer :: xaxis(:), yaxis(:), &
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& zaxis(:), rho(:), rad(:), a(:), &
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& wa(:), abun(:), rhospec(:), da(:)
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integer :: nx, ny, nz, nrho, iskip, irho
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integer :: i, j, k, nspec, nsizes, ii, ai
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character(len=50) :: sizefile, speciesfile, skip
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open(unit=10, file='dustShellInput.in')
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read(10, *) rin, rout
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read(10, *) mdmg
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read(10, *) sizefile
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read(10, *) speciesfile
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read(10, *) nx, ny, nz
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close(10)
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open(unit=10, file='rhoClotho.dat')
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read(10,*) nrho
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allocate(rad(nrho))
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allocate(rho(nrho))
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do i = 1, nrho
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read(10,*) rad(i), rho(i)
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end do
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close(10)
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open(unit=10, file=speciesfile)
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read(10,*) nspec
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allocate(abun(nspec))
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allocate(rhospec(nspec))
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do i = 1, nspec
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read(10,*) skip, abun(i), rhospec(i)
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end do
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close(10)
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open(unit=10, file=sizefile)
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read(10,*) nsizes
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allocate(a(nsizes))
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allocate(wa(nsizes))
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allocate(da(nsizes))
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do i = 1, nsizes
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read(10,*) iskip, a(i), wa(i)
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end do
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close(10)
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if (nSizes>1) then
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da(1) = a(2)-a(1)
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do ai = 2, nSizes-1
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da(ai) = (a(ai+1)-a(ai-1))/2.
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end do
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da(nSizes) = a(nSizes)-a(nSizes-1)
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end if
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normWeight= 0.
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do ai = 1, nSizes
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normWeight = normWeight+wa(ai)*da(ai)
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end do
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if (nSizes>1) then
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do ai = 1, nSizes
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wa(ai) = (wa(ai)*da(ai))/normWeight
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if (.not.wa(ai)>=0.) then
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print*, '! makeDustXSec : Invalid grain weight ', wa(ai), ai
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stop
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end if
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end do
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end if
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print*, ' index, a [um], da [um], weight '
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do ai = 1, nSizes
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print*, ai, real(a(ai)), real(da(ai)), real(wa(ai))
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end do
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a = a*1.e-4 ! cm
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sums = 0.
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do i = 1, nspec
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do j = 1, nsizes
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sums = sums + rhospec(i)*abun(i)*&
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& (4./3.)*Pi*wa(j)*a(j)**3
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enddo
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enddo
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allocate(xaxis(nx+14))
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allocate(yaxis(ny+14))
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allocate(zaxis(nz+14))
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xaxis = 0.
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yaxis = 0.
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zaxis = 0.
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! dx = (rout-rin)/(nx-1)
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! dy = (rout-rin)/(ny-1)
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! dz = (rout-rin)/(nz-1)
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dx = (log10(rout)-log10(rin))/(nx-1)
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dy = (log10(rout)-log10(rin))/(ny-1)
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dz = (log10(rout)-log10(rin))/(nz-1)
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dx1 = rin/14.
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do i = 2, 14
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xaxis(i) = (xaxis(i-1)+dx1)
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end do
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do i = 2, 14
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yaxis(i) = (yaxis(i-1)+dx1)
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end do
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do i = 2, 14
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zaxis(i) = (zaxis(i-1)+dx1)
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end do
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xaxis(2:14) = log10(xaxis(2:14))
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yaxis(2:14) = log10(yaxis(2:14))
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zaxis(2:14) = log10(zaxis(2:14))
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do i = 15, nx+14
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xaxis(i) = log10(rad(i-14))
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end do
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do i = 15, ny+14
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yaxis(i) = log10(rad(i-14))
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end do
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do i = 15, nz+14
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zaxis(i) = log10(rad(i-14))
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end do
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xaxis(2:nx+14) = 10.**xaxis(2:nx+14)
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yaxis(2:nx+14) = 10.**yaxis(2:nx+14)
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zaxis(2:nx+14) = 10.**zaxis(2:nx+14)
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open(unit=12, file = 'ndust.out')
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do i = 1, nx+14
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do j = 1, ny+14
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do k = 1, nz+14
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radius = 1.e10*sqrt( (xaxis(i)/1.e10)*(xaxis(i)/1.e10) + &
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& (yaxis(j)/1.e10)*(yaxis(j)/1.e10) + &
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& (zaxis(k)/1.e10)*(zaxis(k)/1.e10) )
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irho = 0
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do ii = 1, nrho
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if(rad(ii) > radius) then
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irho = ii-1
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exit
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end if
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end do
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if (irho == 0) then
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den = 0.
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elseif (irho ==nrho) then
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den = rho(nrho)
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elseif (irho > 0 .and. irho < nrho) then
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den = rho(irho+1) + (rho(irho)-rho(irho+1))*&
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& (rad(irho+1)-radius)/(rad(irho+1)-rad(irho))
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else
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print*, 'insanity in rho location'
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stop
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end if
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den = den*0.7/1.67d-24
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den = den*3.32d-10
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write(12, *) real(xaxis(i)), real(yaxis(j)), real(zaxis(k)), real(den)
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end do
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end do
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end do
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close(12)
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! print*, mdmg/sums, 3.32d-10*0.7/1.67d-24, (3.32d-10*0.7/1.67d-24)/(mdmg/sums)
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end program makeDustShell

‎accessories/mrnsizes.dat

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28 sizes
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1 5.0000008E-03 1.1313702E+08
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2 5.7795621E-03 6.8134608E+07
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3 6.6806665E-03 4.1032760E+07
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4 7.7222600E-03 2.4711240E+07
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5 8.9262547E-03 1.4881871E+07
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6 1.0317967E-02 8962321.
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7 1.1926661E-02 5397386.
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8 1.3786174E-02 3250475.
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9 1.5935604E-02 1957538.
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10 1.8420158E-02 1178890.
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11 2.1292087E-02 709963.8
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12 2.4611777E-02 427562.5
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13 2.8449053E-02 257491.4
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14 3.2884602E-02 155069.3
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15 3.8011711E-02 93387.56
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16 4.3938190E-02 56240.86
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17 5.0788693E-02 33870.01
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18 5.8707271E-02 20397.57
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19 6.7860432E-02 12284.06
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20 7.8440711E-02 7397.835
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21 9.0670548E-02 4455.209
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22 0.1048072 2683.064
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23 0.1211479 1615.826
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24 0.1400363 973.1000
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25 0.1618697 586.0309
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26 0.1871071 352.9262
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27 0.2162794 212.5430
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28 0.2500000 128.0001
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slope (p): 3.500000

‎accessories/mrnspecies.dat

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2
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'dustData/sil-dlee.nk' 0.5288 3.6
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'dustData/grph2-dl.nk' 0.47 2.2
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'dustData/grph1-dl.nk' 0.1178 2.2

‎accessories/rhoClotho.dat

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50
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4.4800001E+15 1.3687948E-15
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4.9863309E+15 9.1459748E-16
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5.5498880E+15 6.8187640E-16
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6.1771379E+15 5.3306070E-16
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6.8752800E+15 4.2759727E-16
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7.6523261E+15 3.4837793E-16
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8.5171945E+15 2.8665477E-16
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9.4798110E+15 2.3737357E-16
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1.0551222E+16 1.9735550E-16
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1.1743725E+16 1.6447244E-16
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1.3071004E+16 1.3722924E-16
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1.4548293E+16 1.1453396E-16
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1.6192545E+16 9.5562965E-17
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1.8022632E+16 7.9677365E-17
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2.0059557E+16 6.6369333E-17
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2.2326694E+16 5.5226542E-17
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2.4850062E+16 4.5908193E-17
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2.7658625E+16 3.8128579E-17
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3.0784612E+16 3.1645707E-17
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3.4263898E+16 2.6253306E-17
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3.8136415E+16 2.1775053E-17
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4.2446603E+16 1.8060331E-17
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4.7243936E+16 1.4980997E-17
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5.2583461E+16 1.2428760E-17
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5.8526458E+16 1.0312863E-17
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6.5141138E+16 8.5578617E-18
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7.2503412E+16 7.1014266E-18
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8.0697771E+16 5.8922267E-18
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8.9818254E+16 4.8880162E-18
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9.9969539E+16 4.0539758E-18
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1.1126813E+17 3.3613417E-18
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1.2384369E+17 2.7862878E-18
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1.3784054E+17 2.3086652E-18
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1.5341932E+17 1.9122937E-18
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1.7075883E+17 1.5836033E-18
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1.9005804E+17 1.3112292E-18
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2.1153846E+17 1.0856665E-18
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2.3544662E+17 8.9897648E-19
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2.6205686E+17 7.4453751E-19
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2.9167463E+17 6.1683360E-19
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3.2463978E+17 5.1127543E-19
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3.6133065E+17 4.2404928E-19
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4.0216837E+17 3.5198944E-19
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4.4762156E+17 2.9247111E-19
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4.9821191E+17 2.4332022E-19
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5.5451996E+17 2.0273792E-19
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6.1719202E+17 1.6923756E-19
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6.8694724E+17 1.4159198E-19
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7.6458623E+17 1.1878992E-19
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8.5100001E+17 9.9999997E-20

‎benchmarks/dust/1D/p0tau1/input/input.in

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autoPackets 0.20 2. 10000000
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output
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symmetricXYZ
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contShape blackbody
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nebComposition noGas
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maxIterateMC 30 95.
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nPhotons 100000
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nx 16
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ny 16
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nz 16
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LStar 38.26
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Rin 0.
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Rout 2.1800001e17
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TStellar 2500.
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Ndust file 'input/p0tau1.ndust'
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dustFile 'input/p0tau1_grainspecies.dat' 'input/p0tau1_grainsizes.dat'
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writeGrid 80.
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convLimit 0.05
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