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Here is a list of all files with brief descriptions:
abund.cpp
abund.d
abund.h
abund_starburst.cpp
abund_starburst.d
abundances.cpp
abundances.d
age_check.cpp
age_check.d
atmdat.cpp
atmdat.d
atmdat.h
atmdat_2photon.cpp
atmdat_2photon.d
atmdat_3body.cpp
atmdat_3body.d
atmdat_adfa.cpp
atmdat_adfa.d
atmdat_adfa.h
atmdat_char_tran.cpp
atmdat_char_tran.d
atmdat_chianti.cpp
atmdat_chianti.d
atmdat_dielrec_fe.cpp
atmdat_dielrec_fe.d
atmdat_gaunt.cpp
atmdat_gaunt.d
atmdat_gaunt.h
atmdat_HS_caseb.cpp
atmdat_HS_caseb.d
atmdat_lamda.cpp
atmdat_lamda.d
atmdat_lines_setup.cpp
atmdat_lines_setup.d
atmdat_outer_shell.cpp
atmdat_outer_shell.d
atmdat_readin.cpp
atmdat_readin.d
atom_hyperfine.cpp
atom_hyperfine.d
atom_level2.cpp
atom_level2.d
atom_leveln.cpp
atom_leveln.d
atoms.cpp
atoms.d
atoms.h
broke.cpp
broke.d
broke.h
ca.cpp
ca.d
ca.h
called.cpp
called.d
called.h
cddefines.cpp
cddefines.d
cddefines.h
cddefines.h.d
cddrive.cpp
cddrive.d
cddrive.h
cdgetlinelist.cpp
cdgetlinelist.d
cdinit.cpp
cdinit.d
cdstd.h
cloudy.cpp
cloudy.d
cloudy.h
cloudyconfig.h
cloudyconfig_vs.h
co.cpp
co.d
co.h
colden.cpp
colden.d
colden.h
collision.cpp
collision.d
collision.h
cont_createmesh.cpp
cont_createmesh.d
cont_createpointers.cpp
cont_createpointers.d
cont_ffun.cpp
cont_ffun.d
cont_gammas.cpp
cont_gammas.d
cont_ipoint.cpp
cont_ipoint.d
cont_negative.cpp
cont_negative.d
cont_setintensity.cpp
cont_setintensity.d
container_classes.cpp
container_classes.d
container_classes.h
continuum.cpp
continuum.d
continuum.h
conv.cpp
conv.d
conv.h
conv_base.cpp
conv_base.d
conv_eden_ioniz.cpp
conv_eden_ioniz.d
conv_fail.cpp
conv_fail.d
conv_init_solution.cpp
conv_init_solution.d
conv_ioniz.cpp
conv_ioniz.d
conv_itercheck.cpp
conv_itercheck.d
conv_pres_temp_eden_ioniz.cpp
conv_pres_temp_eden_ioniz.d
conv_temp_eden_ioniz.cpp
conv_temp_eden_ioniz.d
cool_dima.cpp
cool_dima.d
cool_etc.cpp
cool_etc.d
cool_eval.cpp
cool_eval.d
cool_eval.h
cool_pr.cpp
cool_pr.d
cool_save.cpp
cool_save.d
coolheavy.cpp
coolheavy.d
coolheavy.h
cooling.h
cosmology.cpp
cosmology.d
cosmology.h
count_ptr.h
cpu.cpp
cpu.d
cpu.h
dark_matter.cpp
dark_matter.d
dark_matter.h
date.h
dense.cpp
dense.d
dense.h
dense_fabden.cpp
dense_fabden.d
dense_parametric_wind.cpp
dense_parametric_wind.d
depth_table.cpp
depth_table.d
depth_table.h
deuterium.cpp
deuterium.d
deuterium.h
doppvel.cpp
doppvel.d
doppvel.h
dynamics.cpp
dynamics.d
dynamics.h
eden_change.cpp
eden_change.d
eden_sum.cpp
eden_sum.d
elementnames.cpp
elementnames.d
elementnames.h
embesq.cpp
embesq.d
embesq.h
emission.cpp
emission.d
emission.h
energy.cpp
energy.d
energy.h
fe.cpp
fe.d
fe.h
flux.cpp
flux.d
flux.h
freebound.cpp
freebound.d
freebound.h
fudgec.cpp
fudgec.d
fudgec.h
gammas.h
generic_state.cpp
generic_state.d
generic_state.h
geometry.cpp
geometry.d
geometry.h
global.cpp
global.d
global.h
grains.cpp
grains.d
grains.h
grains_mie.cpp
grains_mie.d
grains_qheat.cpp
grains_qheat.d
grainvar.cpp
grainvar.d
grainvar.h
gravity.cpp
gravity.d
gravity.h
grid.cpp
grid.d
grid.h
grid_do.cpp
grid_do.d
grid_xspec.cpp
grid_xspec.d
h2.cpp
h2.d
h2.h
h2_priv.h
hcmap.cpp
hcmap.d
hcmap.h
he.cpp
he.d
he.h
heat_save.cpp
heat_save.d
heat_sum.cpp
heat_sum.d
heavy.cpp
heavy.d
heavy.h
helike.h
helike_cs.cpp
helike_cs.d
helike_cs.h
helike_einsta.cpp
helike_einsta.d
helike_einsta.h
helike_energy.cpp
helike_energy.d
helike_recom.cpp
helike_recom.d
helike_recom.h
hextra.cpp
hextra.d
hextra.h
highen.cpp
highen.d
highen.h
hmi.cpp
hmi.d
hmi.h
hydro_bauman.cpp
hydro_bauman.d
hydro_bauman.h
hydro_recom.cpp
hydro_recom.d
hydro_vs_rates.cpp
hydro_vs_rates.d
hydro_vs_rates.h
hydrocollid.cpp
hydrocollid.d
hydroeinsta.cpp
hydroeinsta.d
hydroeinsta.h
hydrogenic.cpp
hydrogenic.d
hydrogenic.h
hydrolevel.cpp
hydrolevel.d
hydrooscilstr.cpp
hydrooscilstr.d
hydrooscilstr.h
hydroreccool.cpp
hydroreccool.d
hyperfine.cpp
hyperfine.d
hyperfine.h
hypho.cpp
hypho.d
hypho.h
init.h
init_coreload.cpp
init_coreload.d
init_coreload_postparse.cpp
init_coreload_postparse.d
init_defaults_preparse.cpp
init_defaults_preparse.d
init_sim_postparse.cpp
init_sim_postparse.d
input.cpp
input.d
input.h
integrate.h
ion_collis.cpp
ion_collis.d
ion_cx.cpp
ion_cx.d
ion_helium.cpp
ion_helium.d
ion_nelem.cpp
ion_nelem.d
ion_photo.cpp
ion_photo.d
ion_recomb.cpp
ion_recomb.d
ion_recomb_Badnell.cpp
ion_recomb_Badnell.d
ion_solver.cpp
ion_solver.d
ion_trim.cpp
ion_trim.d
ion_trim.h
ion_zero.cpp
ion_zero.d
ionbal.cpp
ionbal.d
ionbal.h
ipoint.h
iso.cpp
iso.d
iso.h
iso_collide.cpp
iso_collide.d
iso_continuum_lower.cpp
iso_continuum_lower.d
iso_cool.cpp
iso_cool.d
iso_create.cpp
iso_create.d
iso_error.cpp
iso_error.d
iso_ionize_recombine.cpp
iso_ionize_recombine.d
iso_level.cpp
iso_level.d
iso_photo.cpp
iso_photo.d
iso_radiative_recomb.cpp
iso_radiative_recomb.d
iso_solve.cpp
iso_solve.d
isotopes.cpp
isotopes.d
iter_end_chk.cpp
iter_end_chk.d
iter_startend.cpp
iter_startend.d
iter_track.cpp
iter_track.d
iter_track.h
iterations.cpp
iterations.d
iterations.h
lines.cpp
lines.d
lines.h
lines_service.cpp
lines_service.d
lines_service.h
magnetic.cpp
magnetic.d
magnetic.h
maincl.cpp
maincl.d
mc_escape.cpp
mc_escape.d
mc_escape.h
md5datafile.cpp
md5datafile.d
mean.cpp
mean.d
mean.h
mesh.cpp
mesh.d
mesh.h
mewecoef.cpp
mewecoef.d
mewecoef.h
module.cpp
module.d
module.h
molcol.cpp
molcol.d
molcol.h
mole.cpp
mole.d
mole.h
mole_dissociate.cpp
mole_dissociate.d
mole_drive.cpp
mole_drive.d
mole_eval_balance.cpp
mole_eval_balance.d
mole_h2.cpp
mole_h2.d
mole_h2_coll.cpp
mole_h2_coll.d
mole_h2_create.cpp
mole_h2_create.d
mole_h2_etc.cpp
mole_h2_etc.d
mole_h2_form.cpp
mole_h2_form.d
mole_h2_io.cpp
mole_h2_io.d
mole_priv.h
mole_reactions.cpp
mole_reactions.d
mole_solve.cpp
mole_solve.d
mole_species.cpp
mole_species.d
monitor_results.cpp
monitor_results.d
monitor_results.h
monointerp.cpp
monointerp.d
monointerp.h
mpi_utilities.cpp
mpi_utilities.d
mpi_utilities.h
newton_step.cpp
newton_step.d
newton_step.h
noexec.cpp
noexec.d
noexec.h
numderiv.cpp
numderiv.d
numderiv.h
opacity.cpp
opacity.d
opacity.h
opacity_add1element.cpp
opacity_add1element.d
opacity_add1subshell.cpp
opacity_add1subshell.d
opacity_addtotal.cpp
opacity_addtotal.d
opacity_createall.cpp
opacity_createall.d
opacity_zero.cpp
opacity_zero.d
optimize.cpp
optimize.d
optimize.h
optimize_do.cpp
optimize_do.d
optimize_func.cpp
optimize_func.d
optimize_phymir.cpp
optimize_phymir.d
optimize_subplx.cpp
optimize_subplx.d
oxy.cpp
oxy.d
oxy.h
parse.h
parse_absmag.cpp
parse_absmag.d
parse_abundances.cpp
parse_abundances.d
parse_age.cpp
parse_age.d
parse_agn.cpp
parse_agn.d
parse_atom_h2.cpp
parse_atom_h2.d
parse_atom_iso.cpp
parse_atom_iso.d
parse_backgrd.cpp
parse_backgrd.d
parse_blackbody.cpp
parse_blackbody.d
parse_caseb.cpp
parse_caseb.d
parse_CMB.cpp
parse_CMB.d
parse_commands.cpp
parse_commands.d
parse_compile.cpp
parse_compile.d
parse_constant.cpp
parse_constant.d
parse_coronal.cpp
parse_coronal.d
parse_cosmic_rays.cpp
parse_cosmic_rays.d
parse_cosmology.cpp
parse_cosmology.d
parse_crashdo.cpp
parse_crashdo.d
parse_dlaw.cpp
parse_dlaw.d
parse_dont.cpp
parse_dont.d
parse_drive.cpp
parse_drive.d
parse_element.cpp
parse_element.d
parse_extinguish.cpp
parse_extinguish.d
parse_f_nu.cpp
parse_f_nu.d
parse_fluc.cpp
parse_fluc.d
parse_globule.cpp
parse_globule.d
parse_grain.cpp
parse_grain.d
parse_grid.cpp
parse_grid.d
parse_hden.cpp
parse_hden.d
parse_illuminate.cpp
parse_illuminate.d
parse_init.cpp
parse_init.d
parse_interp.cpp
parse_interp.d
parse_ionpar.cpp
parse_ionpar.d
parse_map.cpp
parse_map.d
parse_metal.cpp
parse_metal.d
parse_norm.cpp
parse_norm.d
parse_optimize.cpp
parse_optimize.d
parse_plot.cpp
parse_plot.d
parse_powerlawcontinuum.cpp
parse_powerlawcontinuum.d
parse_print.cpp
parse_print.d
parse_radius.cpp
parse_radius.d
parse_rangeoption.cpp
parse_rangeoption.d
parse_ratio.cpp
parse_ratio.d
parse_save.cpp
parse_save.d
parse_set.cpp
parse_set.d
parse_species.cpp
parse_species.d
parse_species.h
parse_sphere.cpp
parse_sphere.d
parse_state.cpp
parse_state.d
parse_stop.cpp
parse_stop.d
parse_table.cpp
parse_table.d
parse_test.cpp
parse_test.d
parse_tlaw.cpp
parse_tlaw.d
parse_trace.cpp
parse_trace.d
parser.cpp
parser.d
parser.h
path.h
peimbt.cpp
peimbt.d
peimbt.h
phycon.cpp
phycon.d
phycon.h
physconst.cpp
physconst.d
physconst.h
physconst_template.h
plot.cpp
plot.d
plot.h
predcont.cpp
predcont.d
predcont.h
pressure.cpp
pressure.d
pressure.h
pressure_change.cpp
pressure_change.d
pressure_change.h
pressure_total.cpp
pressure_total.d
proxy_iterator.h
prt.cpp
prt.d
prt.h
prt_alltau.cpp
prt_alltau.d
prt_columns.cpp
prt_columns.d
prt_comment.cpp
prt_comment.d
prt_final.cpp
prt_final.d
prt_header.cpp
prt_header.d
prt_linepres.cpp
prt_linepres.d
prt_lines.cpp
prt_lines.d
prt_lines_continuum.cpp
prt_lines_continuum.d
prt_lines_general.cpp
prt_lines_general.d
prt_lines_grains.cpp
prt_lines_grains.d
prt_lines_helium.cpp
prt_lines_helium.d
prt_lines_hydro.cpp
prt_lines_hydro.d
prt_lines_molecules.cpp
prt_lines_molecules.d
prt_linesum.cpp
prt_linesum.d
prt_meanion.cpp
prt_meanion.d
prt_met.cpp
prt_met.d
prt_zone.cpp
prt_zone.d
quantumstate.cpp
quantumstate.d
quantumstate.h
radius.cpp
radius.d
radius.h
radius_first.cpp
radius_first.d
radius_increment.cpp
radius_increment.d
radius_next.cpp
radius_next.d
rfield.cpp
rfield.d
rfield.h
rt.cpp
rt.d
rt.h
rt_continuum.cpp
rt_continuum.d
rt_continuum_shield_fcn.cpp
rt_continuum_shield_fcn.d
rt_diffuse.cpp
rt_diffuse.d
rt_escprob.cpp
rt_escprob.d
rt_escprob.h
rt_line_all.cpp
rt_line_all.d
rt_line_driving.cpp
rt_line_driving.d
rt_line_one.cpp
rt_line_one.d
rt_line_one_tau_reset.cpp
rt_line_one_tau_reset.d
rt_line_one_tauinc.cpp
rt_line_one_tauinc.d
rt_ots.cpp
rt_ots.d
rt_recom_effic.cpp
rt_recom_effic.d
rt_stark.cpp
rt_stark.d
rt_tau_inc.cpp
rt_tau_inc.d
rt_tau_init.cpp
rt_tau_init.d
rt_tau_reset.cpp
rt_tau_reset.d
sanity_check.cpp
sanity_check.d
save.cpp
save.d
save.h
save_average.cpp
save_average.d
save_do.cpp
save_do.d
save_fits.cpp
save_fits.d
save_line.cpp
save_line.d
save_linedata.cpp
save_linedata.d
save_opacity.cpp
save_opacity.d
save_special.cpp
save_special.d
save_species.cpp
save_species.d
secondaries.cpp
secondaries.d
secondaries.h
service.cpp
service.d
service.h
species.cpp
species.d
species.h
species2.cpp
species2.d
species_pseudo_cont.cpp
species_pseudo_cont.d
stars.cpp
stars.d
stars.h
state.cpp
state.d
state.h
stopcalc.cpp
stopcalc.d
stopcalc.h
struc.cpp
struc.d
struc.h
taulines.cpp
taulines.d
taulines.h
temp_change.cpp
temp_change.d
TestAutoVec.cpp
TestEnergy.cpp
TestFlexArr.cpp
TestFlux.cpp
TestFpCheck.cpp
TestGaunt.cpp
TestInput.cpp
TestIterTrack.cpp
TestMain.cpp
TestMesh.cpp
TestMonoInterp.cpp
TestMultiArr.cpp
TestParser.cpp
TestQuadpack.cpp
TestService.cpp
TestThirdparty.cpp
TestVectorize.cpp
thermal.cpp
thermal.d
thermal.h
thirdparty.cpp
thirdparty.d
thirdparty.h
thirdparty_interpolate.cpp
thirdparty_interpolate.d
thirdparty_lapack.cpp
thirdparty_lapack.d
thirdparty_quadpack.cpp
thirdparty_quadpack.d
thirdparty_quadpack.h
timesc.cpp
timesc.d
timesc.h
trace.cpp
trace.d
trace.h
transition.cpp
transition.d
transition.h
two_photon.cpp
two_photon.d
two_photon.h
vary_input.cpp
vary_input.d
vectorize.cpp
vectorize.d
vectorize.h
vectorize_exp.cpp
vectorize_exp.d
vectorize_exp.h
vectorize_exp_core.h
vectorize_hyper.cpp
vectorize_hyper.d
vectorize_hyper.h
vectorize_hyper_core.h
vectorize_log.cpp
vectorize_log.d
vectorize_log.h
vectorize_log_core.h
vectorize_math.h
vectorize_reduce.cpp
vectorize_reduce.d
vectorize_reduce.h
vectorize_sqrt.cpp
vectorize_sqrt.d
vectorize_sqrt.h
vectorize_sqrt_core.h
version.cpp
version.d
version.h
warnings.cpp
warnings.d
warnings.h
wind.cpp
wind.d
wind.h
yield.h
zero.cpp
zero.d
zone_startend.cpp
zone_startend.d
zones.h
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