Setup python session and notebook¶
We start with importing what we will need. Note here that we want to have matplotlib to do the plot in our notebook! That means we are free to zoom and navigate in the plot even after plotting. Check out different possiblities on your own, please.
In [9]:
%matplotlib inline
import numpy as np
import pencilnew as pcn
import matplotlib.pyplot as plt
Get simulation as object¶
We will use the sample in 'pencil-code/python/tutorials/sample_simulations/2d_streaming_instability' in this notebook. So lets start by reading that simulation in as a simulation object.
In [5]:
SIM = pcn.get_sim('../../sample_simulations/2d_streaming_instability/')
# Creating Simulation object for /home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability
Build the simulation¶
If you havent used this sample before, you may get a warning here that there is no param.nml. Indicating us that the simulation has not been run yet and most functionallity is not given to work so far, of course.
We probaply need to compile this simulation first, make a data dir and run it. We can do that directly from here!
Note: If you want to hide the output after the compilation was done, select that output cell and press O.
In [3]:
%%bash
cd ../../sample_simulations/2d_streaming_instability/
pc_build --cleanall
pc_build
Files will be linked to the root code directory '/home/user/pencil-code'.
Linking job submission/execution scripts.
Linked root Makefile.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'.
No such file: /home/user/pencil-code/src/Makefile.machine
No such file: /home/user/pencil-code/src/.cvsignore
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/special'.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/pre_and_post_processing'.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/magnetic'.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/test_methods'.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/inactive'.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/experimental'.
Linking files in '/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src/initial_condition'.
Rebuilding Makefile from Makefile.src.
(cd src; make FROM_PARENT=src/ -f Makefile.src cleann)
make[1]: Entering directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
rm -f *.x *.o *.a *.mod *.d cparam*.inc cparam_pencils*.inc *.il
rm -f special/*.o special/*.mod
rm -f initial_condition/*.o initial_condition/*.mod
rm -f experimental/*.o experimental/*.mod
rm -f pre_and_post_processing/*.o pre_and_post_processing/*.x
rm -f .current-precision
rm -f *.dot *.ps # Dependency diagram files
rm -f work.pc work.pcl .build*
printf "# %s\n" "Empty" "(This file was written by 'make')" > Makefile.inc
printf "# %s\n" "Empty" "(This file was written by 'make')" > Makefile-standard.inc
rm -f Makefile src/Makefile Makefile_inc TAGS *mpicomm_.f90 mpicomm_double*.f90
rm -rf semiauto-conf_tmp f90_qnd_log_dir
rm -f *.inc && touch Makefile.inc Makefile-standard.inc
make -f Makefile.src Makefile
make[2]: Entering directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
scripts/check-mkfile Makefile.local Makefile.src
env ADAPT_MKFILE= scripts/adapt-mkfile Makefile.src Makefile
make[2]: Leaving directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
make[1]: Leaving directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
MAKING src/Makefile.inc
touch src/.build-history
echo user"@"`hostname` "("`date`")" >> src/.build-history
( cd src && \
echo "===== " make FROM_PARENT=src/ -f Makefile.src code "====="; \
make FROM_PARENT=src/ -f Makefile.src default_to_be \
)
===== make FROM_PARENT=src/ -f Makefile.src code =====
make[1]: Entering directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
scripts/mkcparam -b noborder_profiles.f90 nochemistry.f90 nochiral.f90 nocosmicray.f90 nocosmicrayflux.f90 density.f90 deriv.f90 nodetonate.f90 nodustdensity.f90 nodustvelocity.f90 noentropy.f90 eos_idealgas.f90 nofixed_point.f90 noforcing.f90 nogravity.f90 grid.f90 noheatflux.f90 hydro.f90 nohyperresi_strict.f90 nohypervisc_strict.f90 noimplicit_diffusion.f90 noimplicit_physics.f90 noinitial_condition.f90 nointerstellar.f90 nolorenz_gauge.f90 nomagnetic.f90 magnetic/nomeanfield.f90 magnetic/nomeanfield_demfdt.f90 noneutraldensity.f90 noneutralvelocity.f90 noNSCBC.f90 noopacity.f90 particles_dust.f90 noparticles_adaptation.f90 noparticles_coagulation.f90 noparticles_collisions.f90 particles_map.f90 noparticles_density.f90 noparticles_mass.f90 noparticles_number.f90 noparticles_radius.f90 noparticles_potential.f90 noparticles_grad.f90 noparticles_selfgravity.f90 noparticles_sink.f90 noparticles_drag.f90 noparticles_spin.f90 noparticles_stalker.f90 noparticles_lyapunov.f90 noparticles_stirring.f90 noparticles_diagnos_dv.f90 noparticles_diagnos_state.f90 noparticles_temperature.f90 noparticles_adsorbed.f90 noparticles_surfspec.f90 noparticles_chemistry.f90 nopointmasses.f90 nopoisson.f90 nopolymer.f90 power_spectrum.f90 nopscalar.f90 noradiation.f90 noselfgravity.f90 shear.f90 shock_highorder.f90 nosignal_handling.f90 nosolid_cells.f90 nospecial.f90 nosupersat.f90 nostreamlines.f90 notestfield.f90 notestflow.f90 notestscalar.f90 viscosity.f90 cparam.local -o cparam.inc
${PENCIL_HOME}/utils/pc_identify_revision --reset
make -f Makefile.src start.o run.o combine_videofiles.o read_videofiles.o read_all_videofiles.o read_vectorfiles.o pre_and_post_processing/pc_collect.o pre_and_post_processing/pc_reduce.o pre_and_post_processing/pc_distribute.o pre_and_post_processing/pc_distribute_z.o pre_and_post_processing/pc_extract.o pre_and_post_processing/pc_configtest.o pre_and_post_processing/pc_tecplot.o pre_and_post_processing/pc_tecplot_solid.o start.x run.x combine_videofiles.x read_videofiles.x read_all_videofiles.x read_vectorfiles.x pre_and_post_processing/pc_collect.x pre_and_post_processing/pc_reduce.x pre_and_post_processing/pc_distribute.x pre_and_post_processing/pc_distribute_z.x pre_and_post_processing/pc_extract.x pre_and_post_processing/pc_configtest.x pre_and_post_processing/pc_tecplot.x pre_and_post_processing/pc_tecplot_solid.x
make[2]: Entering directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
if [ "" ]; then \
rm -f cparam.inc; \
rm -f cparam_pencils.inc; \
ln -s cparam.inc cparam.inc; \
ln -s cparam_pencils.inc cparam_pencils.inc; \
fi
sed -e 's/REAL/DOUBLE_PRECISION/g' mpicomm.f90 > mpicomm_double.f90
mpicc -DFUNDERSC=1 -DDOUBLE_PRECISION -o syscalls_ansi.o -c syscalls_ansi.c
scripts/mkdummyinc -d file_io_common.f90 -s file_io_f95.f90 -o file_io_common.inc
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o fftpack.o -c fftpack.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o cparam.o -c cparam.f90
scripts/mkdummyinc -d noinitial_condition.f90 -s noinitial_condition.f90 -o initial_condition_dummies.inc
mpicc -DFUNDERSC=1 -DDOUBLE_PRECISION -o nogsl.o -c nogsl.c
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o cdata.o -c cdata.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o general.o -c general.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o particles_cdata.o -c particles_cdata.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noweno_transport.o -c noweno_transport.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o syscalls.o -c syscalls.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noyinyang.o -c noyinyang.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nompicomm.o -c nompicomm.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o mpicomm_double.o -c mpicomm_double.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o combine_videofiles.o -c combine_videofiles.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o read_videofiles.o -c read_videofiles.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o read_all_videofiles.o -c read_all_videofiles.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o read_vectorfiles.o -c read_vectorfiles.f90
mpif90 read_vectorfiles.o cparam.o cdata.o general.o syscalls.o syscalls_ansi.o nompicomm.o -o read_vectorfiles.x -ldl
mpif90 combine_videofiles.o cparam.o cdata.o general.o syscalls.o syscalls_ansi.o nompicomm.o -o combine_videofiles.x -ldl
mpif90 read_videofiles.o cparam.o cdata.o general.o syscalls.o syscalls_ansi.o nompicomm.o -o read_videofiles.x -ldl
mpif90 read_all_videofiles.o cparam.o cdata.o general.o syscalls.o syscalls_ansi.o nompicomm.o -o read_all_videofiles.x -ldl
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o messages.o -c messages.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o ghost_check.o -c ghost_check.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o deriv.o -c deriv.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o farray.o -c farray.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o file_io_f95.o -c file_io_f95.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noyinyang_mpi.o -c noyinyang_mpi.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o shared_variables.o -c shared_variables.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noimplicit_diffusion.o -c noimplicit_diffusion.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nohdf5_io.o -c nohdf5_io.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o debug_io_dist.o -c debug_io_dist.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_kmeans.o -c noparticles_kmeans.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o sub.o -c sub.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o diagnostics.o -c diagnostics.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o fourier_fftpack.o -c fourier_fftpack.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o io_dist.o -c io_dist.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_stirring.o -c noparticles_stirring.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nolorenz_gauge.o -c nolorenz_gauge.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nodebug.o -c nodebug.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nostreamlines.o -c nostreamlines.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nosignal_handling.o -c nosignal_handling.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nofixed_point.o -c nofixed_point.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o grid.o -c grid.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noborder_profiles.o -c noborder_profiles.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o density_methods.o -c density_methods.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nogravity.o -c nogravity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noinitial_condition.o -c noinitial_condition.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nospecial.o -c nospecial.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o particles_mpicomm.o -c particles_mpicomm.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noopacity.o -c noopacity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nostruct_func.o -c nostruct_func.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o notimeavg.o -c notimeavg.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o magnetic/nomeanfield_demfdt.o -c magnetic/nomeanfield_demfdt.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o magnetic/nomeanfield.o -c magnetic/nomeanfield.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o eos_idealgas.o -c eos_idealgas.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o ghostfold_mpicomm_double.o -c ghostfold_mpicomm_double.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o shear.o -c shear.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o power_spectrum.o -c power_spectrum.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nohyperresi_strict.o -c nohyperresi_strict.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nohypervisc_strict.o -c nohypervisc_strict.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nopoisson.o -c nopoisson.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o initcond.o -c initcond.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nointerstellar.o -c nointerstellar.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o boundcond.o -c boundcond.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o particles_sub.o -c particles_sub.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noheatflux.o -c noheatflux.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o viscosity.o -c viscosity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_number.o -c noparticles_number.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_density.o -c noparticles_density.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_diagnos_state.o -c noparticles_diagnos_state.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_adaptation.o -c noparticles_adaptation.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_potential.o -c noparticles_potential.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_grad.o -c noparticles_grad.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noforcing.o -c noforcing.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nomagnetic.o -c nomagnetic.f90
ar r magnetic.a nomagnetic.o magnetic/nomeanfield.o magnetic/nomeanfield_demfdt.o
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noimplicit_physics.o -c noimplicit_physics.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o shock_highorder.o -c shock_highorder.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nodetonate.o -c nodetonate.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o filter.o -c filter.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nochemistry.o -c nochemistry.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nochiral.o -c nochiral.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nocosmicray.o -c nocosmicray.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o density.o -c density.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nosupersat.o -c nosupersat.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nopscalar.o -c nopscalar.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noradiation.o -c noradiation.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noneutraldensity.o -c noneutraldensity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nopolymer.o -c nopolymer.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noneutralvelocity.o -c noneutralvelocity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_chemistry.o -c noparticles_chemistry.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nolsode_for_chemistry.o -c nolsode_for_chemistry.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noNSCBC.o -c noNSCBC.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nodustvelocity.o -c nodustvelocity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nodustdensity.o -c nodustdensity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_radius.o -c noparticles_radius.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_temperature.o -c noparticles_temperature.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_mass.o -c noparticles_mass.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_spin.o -c noparticles_spin.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_adsorbed.o -c noparticles_adsorbed.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_surfspec.o -c noparticles_surfspec.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noentropy.o -c noentropy.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o hydro.o -c hydro.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nosolid_cells.o -c nosolid_cells.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o particles_map.o -c particles_map.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_drag.o -c noparticles_drag.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_collisions.o -c noparticles_collisions.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_diagnos_dv.o -c noparticles_diagnos_dv.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_coagulation.o -c noparticles_coagulation.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_selfgravity.o -c noparticles_selfgravity.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_sink.o -c noparticles_sink.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_stalker.o -c noparticles_stalker.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noparticles_lyapunov.o -c noparticles_lyapunov.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o particles_dust.o -c particles_dust.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o particles_main.o -c particles_main.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o notestscalar.o -c notestscalar.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o notestfield.o -c notestfield.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o notestflow.o -c notestflow.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o persist.o -c persist.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o slices.o -c slices.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nopointmasses.o -c nopointmasses.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o noselfgravity.o -c noselfgravity.f90
ar r particles_main.a particles_dust.o noparticles_adaptation.o particles_cdata.o noparticles_coagulation.o noparticles_collisions.o noparticles_kmeans.o particles_main.o particles_map.o noparticles_density.o particles_mpicomm.o noparticles_number.o particles_dust.o noparticles_potential.o noparticles_radius.o noparticles_grad.o noparticles_selfgravity.o noparticles_sink.o noparticles_spin.o noparticles_temperature.o noparticles_mass.o noparticles_chemistry.o noparticles_adsorbed.o noparticles_surfspec.o noparticles_stalker.o noparticles_lyapunov.o noparticles_stirring.o particles_sub.o noparticles_diagnos_dv.o noparticles_diagnos_state.o noparticles_drag.o
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o snapshot.o -c snapshot.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o nocosmicrayflux.o -c nocosmicrayflux.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o equ.o -c equ.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o timestep.o -c timestep.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pencil_check.o -c pencil_check.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o notestperturb.o -c notestperturb.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o param_io.o -c param_io.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o register.o -c register.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o start.o -c start.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o run.o -c run.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_collect.o -c pre_and_post_processing/pc_collect.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_reduce.o -c pre_and_post_processing/pc_reduce.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_distribute.o -c pre_and_post_processing/pc_distribute.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_distribute_z.o -c pre_and_post_processing/pc_distribute_z.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_extract.o -c pre_and_post_processing/pc_extract.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_configtest.o -c pre_and_post_processing/pc_configtest.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_tecplot.o -c pre_and_post_processing/pc_tecplot.f90
mpif90 -O -fdefault-real-8 -fdefault-double-8 -o pre_and_post_processing/pc_tecplot_solid.o -c pre_and_post_processing/pc_tecplot_solid.f90
mpif90 pre_and_post_processing/pc_distribute_z.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_distribute_z.x -ldl
mpif90 pre_and_post_processing/pc_distribute.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_distribute.x -ldl
mpif90 pre_and_post_processing/pc_configtest.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_configtest.x -ldl
mpif90 pre_and_post_processing/pc_collect.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_collect.x -ldl
mpif90 pre_and_post_processing/pc_tecplot_solid.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_tecplot_solid.x -ldl
mpif90 pre_and_post_processing/pc_tecplot.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_tecplot.x -ldl
mpif90 nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a noborder_profiles.o boundcond.o cdata.o cparam.o nodebug.o debug_io_dist.o deriv.o diagnostics.o farray.o filter.o nofixed_point.o fourier_fftpack.o general.o ghost_check.o ghostfold_mpicomm_double.o grid.o nogsl.o noimplicit_diffusion.o initcond.o noinitial_condition.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o messages.o mpicomm_double.o noNSCBC.o param_io.o persist.o power_spectrum.o register.o shared_variables.o nosignal_handling.o slices.o snapshot.o nosolid_cells.o nostreamlines.o nostruct_func.o sub.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a start.o fftpack.o -o start.x -ldl
mpif90 pre_and_post_processing/pc_extract.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_extract.x -ldl
mpif90 nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a noborder_profiles.o boundcond.o cdata.o cparam.o nodebug.o debug_io_dist.o deriv.o diagnostics.o farray.o filter.o nofixed_point.o fourier_fftpack.o general.o ghost_check.o ghostfold_mpicomm_double.o grid.o nogsl.o noimplicit_diffusion.o initcond.o noinitial_condition.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o messages.o mpicomm_double.o noNSCBC.o param_io.o persist.o power_spectrum.o register.o shared_variables.o nosignal_handling.o slices.o snapshot.o nosolid_cells.o nostreamlines.o nostruct_func.o sub.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a timestep.o equ.o pencil_check.o run.o fftpack.o -o run.x -ldl
mpif90 pre_and_post_processing/pc_reduce.o nochemistry.o nochiral.o nocosmicray.o nocosmicrayflux.o density.o density_methods.o nodetonate.o nodustdensity.o nodustvelocity.o noentropy.o eos_idealgas.o noforcing.o nogravity.o noheatflux.o hydro.o nohyperresi_strict.o nohypervisc_strict.o noimplicit_physics.o nointerstellar.o nolorenz_gauge.o noneutraldensity.o noneutralvelocity.o noopacity.o nopointmasses.o nopoisson.o nopolymer.o nopscalar.o noradiation.o noselfgravity.o shear.o shock_highorder.o nospecial.o nosupersat.o notestfield.o notestflow.o notestscalar.o viscosity.o magnetic.a particles_main.a boundcond.o noborder_profiles.o nodebug.o deriv.o fourier_fftpack.o ghostfold_mpicomm_double.o grid.o nogsl.o noinitial_condition.o debug_io_dist.o nohdf5_io.o io_dist.o file_io_f95.o nolsode_for_chemistry.o nompicomm.o noNSCBC.o power_spectrum.o nosignal_handling.o slices.o nosolid_cells.o nostruct_func.o syscalls.o syscalls_ansi.o notestperturb.o notimeavg.o noweno_transport.o cdata.o cparam.o diagnostics.o farray.o filter.o initcond.o messages.o general.o param_io.o persist.o register.o shared_variables.o snapshot.o nostreamlines.o sub.o noyinyang.o noyinyang_mpi.o magnetic.a particles_main.a ghost_check.o noimplicit_diffusion.o equ.o fftpack.o -o pre_and_post_processing/pc_reduce.x -ldl
make[2]: Leaving directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
${PENCIL_HOME}/utils/pc_identify_revision
make[1]: Leaving directory `/home/user/pencil-code/python/tutorials/sample_simulations/2d_streaming_instability/src'
Found config file </home/user/pencil-code/config/hosts/aschreiber/host-vm-think-aschreiber-GNU_Linux-Welcome.conf>
Found config file </home/user/pencil-code/config/hosts/aschreiber/host-vm-think-aschreiber-GNU_Linux-Welcome.conf>
Running make '-j' 'FFLAGS_DOUBLE=-fdefault-real-8 -fdefault-double-8' 'CFLAGS_DOUBLE=-DDOUBLE_PRECISION' 'LD_MPI=' 'CFLAGS_FFTW3=' 'FFLAGS_FFTW3=' 'LD_FFTW3=' 'CFLAGS_FFTW2=' 'FFLAGS_FFTW2=' 'LD_FFTW2=' 'FC=mpif90' 'F77=mpif77' 'FFLAGS=-O' 'FSTD_95=' 'FSTD_2003=-std=f2003' 'CC=mpicc' 'CFLAGS=-DFUNDERSC=1' 'default_to_be'
precision-check: No such file src/.current-precision -- creating new one at ./src/scripts/precision-check line 36.
fftpack.f90:154.33:
call passb4 ( 2*ido, l1, c, ch, wa(iw), wa(ix2), wa(ix3) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:156.33:
call passb4 ( 2*ido, l1, ch, c, wa(iw), wa(ix2), wa(ix3) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:164.33:
call passb2 ( 2*ido, l1, c, ch, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:166.33:
call passb2 ( 2*ido, l1, ch, c, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:176.33:
call passb3 ( 2*ido, l1, c, ch, wa(iw), wa(ix2) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:178.33:
call passb3 ( 2*ido, l1, ch, c, wa(iw), wa(ix2) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:190.33:
call passb5 ( 2*ido, l1, c, ch, wa(iw), wa(ix2), wa(ix3), wa(ix4) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:192.33:
call passb5 ( 2*ido, l1, ch, c, wa(iw), wa(ix2), wa(ix3), wa(ix4) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:200.47:
call passb ( nac, 2*ido, ip, l1, idl1, c, c, c, ch, ch, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:202.47:
call passb ( nac, 2*ido, ip, l1, idl1, ch, ch, ch, c, c, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:76.22:
call cfftb1 ( n, c, wsave(1), wsave(2*n+1), wsave(4*n+1) )
1
Warning: Type mismatch in argument 'ch' at (1); passed REAL(8) to COMPLEX(8)
fftpack.f90:447.33:
call passf4 ( 2*ido, l1, c, ch, wa(iw), wa(ix2), wa(ix3) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:449.33:
call passf4 ( 2*ido, l1, ch, c, wa(iw), wa(ix2), wa(ix3) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:457.33:
call passf2 ( 2*ido, l1, c, ch, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:459.33:
call passf2 ( 2*ido, l1, ch, c, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:469.33:
call passf3 ( 2*ido, l1, c, ch, wa(iw), wa(ix2) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:471.33:
call passf3 ( 2*ido, l1, ch, c, wa(iw), wa(ix2) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:483.33:
call passf5 ( 2*ido, l1, c, ch, wa(iw), wa(ix2), wa(ix3), wa(ix4) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:485.33:
call passf5 ( 2*ido, l1, ch, c, wa(iw), wa(ix2), wa(ix3), wa(ix4) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:493.47:
call passf ( nac, 2*ido, ip, l1, idl1, c, c, c, ch, ch, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:495.47:
call passf ( nac, 2*ido, ip, l1, idl1, ch, ch, ch, c, c, wa(iw) )
1
Warning: Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8)
fftpack.f90:370.22:
call cfftf1 ( n, c, wsave(1), wsave(2*n+1), wsave(4*n+1) )
1
Warning: Type mismatch in argument 'ch' at (1); passed REAL(8) to COMPLEX(8)
fftpack.f90:645.33:
call cffti1 ( n, wsave(2*n+1), wsave(4*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:6575.44:
call rfftb1 ( n, r, wsave(1), wsave(n+1), wsave(2*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:6802.44:
call rfftf1 ( n, r, wsave(1), wsave(n+1), wsave(2*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:6999.31:
call rffti1 ( n, wsave(n+1), wsave(2*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:2248.44:
call dfftf1 ( n, r, wsave(1), wsave(n+1), wsave(2*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:2445.31:
call dffti1 ( n, wsave(n+1), wsave(2*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:2680.56:
call dsint1 ( n, x, wsave(1), wsave(iw1), wsave(iw2), wsave(iw3) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:3357.34:
call ezffti1 ( n, wsave(2*n+1), wsave(3*n+1) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
fftpack.f90:8147.56:
call rsint1 ( n, x, wsave(1), wsave(iw1), wsave(iw2), wsave(iw3) )
1
Warning: Type mismatch in argument 'ifac' at (1); passed REAL(8) to INTEGER(4)
mpicomm_double.f90:8394.20:
do i=2,ncpus
1
Warning: DO loop at (1) will be executed zero times
mpicomm_double.f90:8226.29:
do px = 1, nprocx-1
1
Warning: DO loop at (1) will be executed zero times
mpicomm_double.f90:8235.29:
do py = 1, nprocy-1
1
Warning: DO loop at (1) will be executed zero times
mpicomm_double.f90:8244.29:
do pz = 1, nprocz-1
1
Warning: DO loop at (1) will be executed zero times
mpicomm_double.f90:4261.22:
do i=1,ncpus-1 ! send permission, wait for success message
1
Warning: DO loop at (1) will be executed zero times
farray.f90:388.21:
do i=1,mscratch
1
Warning: DO loop at (1) will be executed zero times
fourier_fftpack.f90:4077.32:
do ipy_from=1,nprocy-1
1
Warning: DO loop at (1) will be executed zero times
fourier_fftpack.f90:4151.32:
do ipy_to=1,nprocy-1
1
Warning: DO loop at (1) will be executed zero times
fourier_fftpack.f90:3927.34:
do ipy_send=1,nprocy-1
1
Warning: DO loop at (1) will be executed zero times
fourier_fftpack.f90:3950.34:
do ipy_send=1,nprocy-1
1
Warning: DO loop at (1) will be executed zero times
fourier_fftpack.f90:3971.34:
do ipy_send=1,nprocy-1
1
Warning: DO loop at (1) will be executed zero times
fourier_fftpack.f90:3994.34:
do ipy_send=1,nprocy-1
1
Warning: DO loop at (1) will be executed zero times
particles_mpicomm.f90:218.35:
do jspec=2,npar_species-1
1
Warning: DO loop at (1) will be executed zero times
power_spectrum.f90:2096.22:
spectrum(1)=(bbtemp(1)*bbtemp(1))&
1
Warning: Array reference at (1) is out of bounds (1 > 0) in dimension 1
power_spectrum.f90:2098.25:
spectrumhel(1)=(aatemp(1)*bbtemp(1))&
1
Warning: Array reference at (1) is out of bounds (1 > 0) in dimension 1
power_spectrum.f90:2100.32:
do ispec=2,nzgrid/2
1
Warning: DO loop at (1) will be executed zero times
power_spectrum.f90:2110.25:
spectrumhel(nzgrid/2)=(aatemp(nzgrid)*bbtemp(nzgrid))&
1
Warning: Array reference at (1) is out of bounds (0 < 1) in dimension 1
power_spectrum.f90:2112.22:
spectrum(nzgrid/2)=(bbtemp(nzgrid)*bbtemp(nzgrid))&
1
Warning: Array reference at (1) is out of bounds (0 < 1) in dimension 1
power_spectrum.f90:1932.23:
spectrum(1)=(aatemp(1)**2)&
1
Warning: Array reference at (1) is out of bounds (1 > 0) in dimension 1
power_spectrum.f90:1934.33:
do ispec=2,nzgrid/2
1
Warning: DO loop at (1) will be executed zero times
power_spectrum.f90:1940.23:
spectrum(nzgrid/2)=(aatemp(nzgrid)**2)&
1
Warning: Array reference at (1) is out of bounds (0 < 1) in dimension 1
initcond.f90:5844.30:
do icpu=nprocy+1,ncpus
1
Warning: DO loop at (1) will be executed zero times
initcond.f90:5772.30:
do icpu=nprocy+1,ncpus
1
Warning: DO loop at (1) will be executed zero times
initcond.f90:5554.28:
do py = 1, nprocxy-1
1
Warning: DO loop at (1) will be executed zero times
initcond.f90:5576.29:
do pz = 1, nprocz-1
1
Warning: DO loop at (1) will be executed zero times
boundcond.f90:7957.25:
do j=1,nprocx-1
1
Warning: DO loop at (1) will be executed zero times
boundcond.f90:7980.27:
do j=1,nprocx-1
1
Warning: DO loop at (1) will be executed zero times
boundcond.f90:5305.24:
do i=1,nprocxy-1
1
Warning: DO loop at (1) will be executed zero times
boundcond.f90:5432.28:
do py=1, nprocxy-1
1
Warning: DO loop at (1) will be executed zero times
ar: creating magnetic.a
ar: creating particles_main.a
Make data dir and run¶
Simlation should now be compiled. We need a datadirectory now and are ready to run!
Note: If you want to hide the output after the compilation was done, select that output cell and press O.
In [2]:
%%bash
cd ../../sample_simulations/2d_streaming_instability/
mkdir data
pc_run
hostname = vm-think-aschreiber
MPI run
1 CPU
1 node, 1 CPU per node
lparticles = 1
lpointmasses = 0
Revision: f26ffba96791ede3b6310b4ba7a9a8208df5b077
D .gitignore
M python/tutorials/README_FIRST
Fri Dec 16 11:56:49 2016
Running under MPI
Running '/usr/bin/time -p mpiexec -n 1 ./src/run.x'...
SVN: ------- v. ( ) $Id$
SVN: start.in v. 9840 (2008-09-05 07:29:37) ajohan
SVN: start.in v. 9840 (2008-09-05 07:29:37) ajohan
initialize_mpicomm: enabled MPI
SVN: ------- v. ( ) $Id$
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The verbose level is ip= 14 (ldebug= F )
This is a 2-D run
nxgrid, nygrid, nzgrid= 16 16 1
Lx, Ly, Lz= 0.10000000000000001 0.10000000000000001 0.10000000000000001
Vbox= 1.0000000000000002E-002
setup_slices: slice_position = m
setup_slices: ix,iy,iz,iz2 (video files) = -1 -1 -1 -1
units_general: unit_velocity= 1.0000000000000000
units_general: unit_density= 1.0000000000000000
units_general: unit_length= 1.0000000000000000
units_general: unit_magnetic= 3.5449077018110318
units_eos: unit_temperature= 1.2027220936797545E-008
units_eos: cp, lnTT0, cs0, pp0= 1.0000000000000000 0.0000000000000000 1.0000000000000000 1.0000000000000000
(x,y,z)(point)= -3.1249999999999958E-003 -3.1249999999999958E-003 0.0000000000000000
(x,y,z)(point2)= -4.0625000000000001E-002 -4.0625000000000001E-002 0.0000000000000000
diffusion: (d^6/dx^6+d^6/dy^6+d^6/dz^6)rho
diffusion: shock diffusion
select_eos_variable: Using rho and cs2
initialize_energy: Global density gradient with beta_glnrho_global= -0.10000000000000001 0.0000000000000000 0.0000000000000000
viscous force: nu*(del6u+S.glnrho)
viscous force: nu_shock*(XXXXXXXXXXX)
initialize_particles: dust-to-gas ratio eps_dtog= 1.0000000000000000
initialize_particles: mass per constituent particle mpmat= 0.0000000000000000
initialize_particles: mass per superparticle mp_swarm = 3.9062500000000009E-006
initialize_particles: number density per superparticle np_swarm= 0.0000000000000000
initialize_particles: mass density per superparticle rhop_swarm= 0.10000000000000001
initialize particles: set minimum collisional time-scale equal to two times the Courant time-step.
initialize_particles_map: selected triangular-shaped-cloud for particle-mesh method.
choose_pencils: finding out which pencils are needed for the pencil case
write_pencil_info: pencil information written to the file pencils.list
Maximum simulation time exceeded
Simulation finished after 0 time-steps
Writing final snapshot at time t = 12.000818451881171
Wall clock time [hours] = 7.540E-06 (+/- 2.78E-10)
Fri Dec 16 11:56:49 2016
Running
pc_deprecated_slice_links
mkdir: cannot create directory ‘data’: File exists Found config file </home/user/pencil-code/config/hosts/aschreiber/host-vm-think-aschreiber-GNU_Linux-Welcome.conf> Subcommand: run real 0.09 user 0.06 sys 0.02
Read timeseries¶
Thats already it! Lets get the timeseries and plot it!
Note: If you want to suppress output from a python command, append ; to that line.
In [6]:
ts = pcn.read.ts(datadir = SIM.datadir);
Read 370 lines
In [13]:
fig, ax = plt.subplots(1,1)
ax.plot(ts.t, ts.rhopmax)
ax.set_xlabel(r'$t$')
ax.set_ylabel(r'$\rho_\mathrm{p,max}$')
Out[13]:
<matplotlib.text.Text at 0x4fc2450>
See available content of timeseries¶
The timeseries object stores all you available quantity timeseries. To get an overview use ts.
In [23]:
print([s for s in dir(ts) if not s.startswith('__')])
['Mamax', 'Marms', 'cs', 'csm', 'dt', 'ekin', 'ekinp', 'ekintot', 'it', 'keys', 'nparmax', 'npm', 'npmax', 'npmin', 'read', 'rhom', 'rhomax', 'rhomin', 'rhopm', 'rhopmax', 'rhopmin', 'ruxuym', 't', 'u2m', 'um2', 'umax', 'urms', 'uu', 'ux2m', 'uxm', 'uxuym', 'uy2m', 'uym', 'uz2m', 'uzm', 'vpmax', 'vpx2m', 'vpxm', 'vpy2m', 'vpym', 'vpz2m', 'vpzm', 'walltime']
Plot all density timeseries in two lines¶
In [28]:
for q in dir(ts):
if q.startswith('rho'): plt.plot(ts.t, getattr(ts, q))
