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Genchiaki merge2 #143

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511a539
Metal chemistry, grain growth
genchiaki Jun 22, 2020
bdfa14f
enable multi metals
genchiaki Jun 29, 2020
88f7720
modify solver of grain temperature
genchiaki Jul 10, 2020
eecb3ad
correct gasgr
genchiaki Jul 10, 2020
38116eb
correct confliction of parameters
genchiaki Jul 17, 2020
1d5c9e3
more stable at high density and temperature
genchiaki Jul 25, 2020
f03bdf3
correct convergence criteria
genchiaki Jul 26, 2020
c2c344a
correct chunit
genchiaki Jul 27, 2020
8b6f008
correct a fatal error in scale_fields_g (only for comoving)
genchiaki Jul 28, 2020
f3977a5
correct for SMBH radiation problem
genchiaki Jul 29, 2020
62bfa64
make consistency of dust density
genchiaki Jul 31, 2020
29d8998
for NAOJ
genchiaki Aug 4, 2020
973ba10
correct chunit
genchiaki Aug 5, 2020
e21a272
correct chunit for iexpand = 1 (final)
genchiaki Aug 6, 2020
88ec27d
comment out write statements
genchiaki Aug 6, 2020
eb8f4ee
correct chunit for cosmology simulations
genchiaki Aug 11, 2020
b833c9d
convergence criteria for imp_eng = 0
genchiaki Aug 13, 2020
7afaa2e
convergence criteria for imp_eng = 0 II
genchiaki Aug 13, 2020
0c24be5
convergence criteria for imp_eng = 0 III
genchiaki Aug 20, 2020
ef01ada
multi metals
genchiaki Aug 31, 2020
6b79d74
correct ceiling_species for multi_metals
genchiaki Sep 8, 2020
dd3c4e5
correct error in ceiling_species
genchiaki Sep 14, 2020
fab8734
metal ionization/dissociation
genchiaki Jan 17, 2021
6a4f1a9
correction
genchiaki Apr 12, 2021
2b233d9
Merge remote-tracking branch 'genchiaki/metal-dust-radiation' into ge…
EwanBJones98 Sep 22, 2022
7faef62
Merged genchiaki's pull request into master. Not yet compiled or tested.
EwanBJones98 Sep 22, 2022
ea06a25
Added rates moved from calc_rates_g.F to rate_functions.c (in last co…
Oct 2, 2022
56f04eb
Began pygrackle update for merge
Nov 10, 2022
29fe448
Merged master into branch
Nov 10, 2022
963961d
Fixing bugs in pygrackle merge
Nov 11, 2022
ae8cf65
Pygrackle wrapper now compiles. Ready for testing!
Nov 14, 2022
c7ec575
modify several parts
genchiaki Mar 23, 2023
4cce99f
tests cleared
genchiaki Mar 23, 2023
864ed4c
Merging with main.
brittonsmith Apr 18, 2023
00bbbb0
Merger remnants.
brittonsmith Apr 18, 2023
7f7e08b
fix a conflict
genchiaki May 17, 2023
8eebcca
Merge branch 'main' into genchiaki_merge2
brittonsmith May 19, 2023
76a431b
Revert changes to linux make file.
brittonsmith May 22, 2023
a1e7588
Update src/clib/initialize_rates.c
genchiaki May 27, 2023
d289462
answer to comments/questions
genchiaki Jun 5, 2023
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23 changes: 20 additions & 3 deletions src/clib/Make.config.objects
Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,6 @@ OBJS_CONFIG_LIB = \
calculate_temperature.lo \
calc_temp1d_cloudy_g.lo \
calc_temp_cloudy_g.lo \
calc_tdust_1d_g.lo \
calc_tdust_3d_g.lo \
cool1d_cloudy_g.lo \
cool1d_cloudy_old_tables_g.lo \
cool1d_multi_g.lo \
Expand All @@ -38,5 +36,24 @@ OBJS_CONFIG_LIB = \
solve_chemistry.lo \
solve_rate_cool_g.lo \
update_UVbackground_rates.lo \
calc_rates_metal.lo \
calc_rates_dust.lo \
calc_rates_dust_loc.lo \
calc_rates_dust_C13.lo \
calc_rates_dust_C20.lo \
calc_rates_dust_C25.lo \
calc_rates_dust_C30.lo \
calc_rates_dust_F13.lo \
calc_rates_dust_F15.lo \
calc_rates_dust_F50.lo \
calc_rates_dust_F80.lo \
calc_rates_dust_P170.lo \
calc_rates_dust_P200.lo \
calc_rates_dust_Y19.lo \
lookup_cool_rates0d.lo \
calc_tdust_1d_g.lo \
calc_tdust_3d_g.lo \
calc_grain_size_increment_1d.lo \
rate_functions.lo \
initialize_rates.lo
initialize_rates.lo \
gaussj_g.lo
88 changes: 88 additions & 0 deletions src/clib/Make.mach.ATERUI
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
#=======================================================================
#
# FILE: Make.mach.linux-gnu
#
# DESCRIPTION: Makefile settings for a machine running Ubuntu
#
# AUTHOR: Rick Wagner ([email protected])
#
# DATE: 2008-09-16
#
# This configuration assumes that build-essentials, gfortran,
# OpenMPI and HDF5 have been installed using apt-get.
#
#=======================================================================

MACH_TEXT = CfCA aterui with cray compilers. \
Do this: module load cray-hdf5
MACH_VALID = 1
MACH_FILE = Make.mach.ATERUI

#-----------------------------------------------------------------------
# Install paths (local variables)
#-----------------------------------------------------------------------

LOCAL_HDF5_INSTALL = $(HDF5_DIR)

#-----------------------------------------------------------------------
# Compiler settings
#-----------------------------------------------------------------------

MACH_CC_NOMPI = cc # C compiler
MACH_CXX_NOMPI = CC # C++ compiler
MACH_FC_NOMPI = ftn # Fortran 77
MACH_F90_NOMPI = ftn # Fortran 90
MACH_LD_NOMPI = cc # Linker
MACH_LIBTOOL = libtool

#-----------------------------------------------------------------------
# Machine-dependent defines
#-----------------------------------------------------------------------

MACH_DEFINES = -DLINUX -DH5_USE_16_API -std=c11 -h fp3 -Wno-unknown-pragmas

#-----------------------------------------------------------------------
# Compiler flag settings
#-----------------------------------------------------------------------

MACH_OMPFLAGS = #-fopenmp
MACH_CPPFLAGS = -P -traditional
MACH_CFLAGS =
MACH_CXXFLAGS =
MACH_FFLAGS =
MACH_F90FLAGS =
MACH_LDFLAGS =

#-----------------------------------------------------------------------
# Optimization flags
#-----------------------------------------------------------------------

MACH_OPT_WARN = -Wall -g
MACH_OPT_DEBUG = -g
MACH_OPT_HIGH = -O2
MACH_OPT_AGGRESSIVE = -O3 -g

#-----------------------------------------------------------------------
# Includes
#-----------------------------------------------------------------------

LOCAL_INCLUDES_HDF5 = -I$(LOCAL_HDF5_INSTALL)/include # HDF5 includes

MACH_INCLUDES = $(LOCAL_INCLUDES_HDF5)

#-----------------------------------------------------------------------
# Libraries
#-----------------------------------------------------------------------

LOCAL_LIBS_HDF5 = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 # HDF5 libraries
LOCAL_LIBS_MACH =

MACH_LIBS = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)

#-----------------------------------------------------------------------
# Installation
#-----------------------------------------------------------------------

MACH_INSTALL_PREFIX = /work/nakazatoyr/usr/local
MACH_INSTALL_LIB_DIR =
MACH_INSTALL_INCLUDE_DIR =
88 changes: 88 additions & 0 deletions src/clib/Make.mach.hive-gcc
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
#=======================================================================
#
# FILE: Make.mach.linux-gnu
#
# DESCRIPTION: Makefile settings for a machine running Ubuntu 8.04
#
# AUTHOR: Rick Wagner ([email protected])
#
# DATE: 2008-09-16
#
# This configuration assumes that build-essentials, gfortran,
# OpenMPI and HDF5 have been installed using apt-get.
#
#=======================================================================

MACH_TEXT = Georgia Tech HIVE (GNU)
MACH_VALID = 1
MACH_FILE = Make.mach.hive-gcc

#-----------------------------------------------------------------------
# Install paths (local variables)
#-----------------------------------------------------------------------

LOCAL_HDF5_INSTALL = $(HOME)/usr/local/
#LOCAL_HDF5_INSTALL = /storage/home/hhive1/jw254/local/
#LOCAL_HDF5_INSTALL = /usr/local/pacerepov1/hdf5/1.8.19/mvapich2-2.1/intel-15.0

#-----------------------------------------------------------------------
# Compiler settings
#-----------------------------------------------------------------------

MACH_CC_NOMPI = gcc # C compiler
MACH_CXX_NOMPI = g++ # C++ compiler
MACH_FC_NOMPI = gfortran # Fortran 77
MACH_F90_NOMPI = gfortran # Fortran 90
MACH_LD_NOMPI = gcc # Linker
MACH_LIBTOOL = libtool

#-----------------------------------------------------------------------
# Machine-dependent defines
#-----------------------------------------------------------------------

MACH_DEFINES = -DLINUX -DH5_USE_16_API -fPIC

#-----------------------------------------------------------------------
# Compiler flag settings
#-----------------------------------------------------------------------

MACH_CPPFLAGS = -P -traditional
MACH_CFLAGS =
MACH_CXXFLAGS =
MACH_FFLAGS = -fno-second-underscore -ffixed-line-length-132
MACH_F90FLAGS = -fno-second-underscore
MACH_LDFLAGS =

#-----------------------------------------------------------------------
# Optimization flags
#-----------------------------------------------------------------------

MACH_OPT_WARN = -Wall -g
MACH_OPT_DEBUG = -g
MACH_OPT_HIGH = -O2
MACH_OPT_AGGRESSIVE = -O3 -g

#-----------------------------------------------------------------------
# Includes
#-----------------------------------------------------------------------

LOCAL_INCLUDES_HDF5 = -I$(LOCAL_HDF5_INSTALL)/include # HDF5 includes

MACH_INCLUDES = $(LOCAL_INCLUDES_HDF5)

#-----------------------------------------------------------------------
# Libraries
#-----------------------------------------------------------------------

LOCAL_LIBS_HDF5 = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 -lz # HDF5 libraries
LOCAL_LIBS_MACH = -lgfortran # Machine-dependent libraries

MACH_LIBS = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)

#-----------------------------------------------------------------------
# Installation
#-----------------------------------------------------------------------

MACH_INSTALL_PREFIX = $(HOME)/usr/local
MACH_INSTALL_LIB_DIR =
MACH_INSTALL_INCLUDE_DIR =
88 changes: 88 additions & 0 deletions src/clib/Make.mach.hive-intel
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
#=======================================================================
#
# FILE: Make.mach.linux-gnu
#
# DESCRIPTION: Makefile settings for a machine running Ubuntu 8.04
#
# AUTHOR: Rick Wagner ([email protected])
#
# DATE: 2008-09-16
#
# This configuration assumes that build-essentials, gfortran,
# OpenMPI and HDF5 have been installed using apt-get.
#
#=======================================================================

MACH_TEXT = Georgia Tech HIVE (INTEL)
MACH_VALID = 1
MACH_FILE = Make.mach.hive-intel

#-----------------------------------------------------------------------
# Install paths (local variables)
#-----------------------------------------------------------------------

LOCAL_HDF5_INSTALL = $(HOME)/usr/local/
#LOCAL_HDF5_INSTALL = /storage/home/hhive1/jw254/local/
#LOCAL_HDF5_INSTALL = /usr/local/pacerepov1/hdf5/1.8.19/mvapich2-2.1/intel-15.0

#-----------------------------------------------------------------------
# Compiler settings
#-----------------------------------------------------------------------

MACH_CC_NOMPI = mpiicc # C compiler
MACH_CXX_NOMPI = mpiicpc # C++ compiler
MACH_FC_NOMPI = mpiifort # Fortran 77
MACH_F90_NOMPI = mpiifort # Fortran 90
MACH_LD_NOMPI = mpiicc # Linker
MACH_LIBTOOL = libtool

#-----------------------------------------------------------------------
# Machine-dependent defines
#-----------------------------------------------------------------------

MACH_DEFINES = -DLINUX -DH5_USE_16_API -fPIC

#-----------------------------------------------------------------------
# Compiler flag settings
#-----------------------------------------------------------------------

MACH_CPPFLAGS = -P -traditional
MACH_CFLAGS =
MACH_CXXFLAGS =
MACH_FFLAGS = -132
MACH_F90FLAGS =
MACH_LDFLAGS = -lifcore -lifport -lpthread -ldl

#-----------------------------------------------------------------------
# Optimization flags
#-----------------------------------------------------------------------

MACH_OPT_WARN = -Wall -g
MACH_OPT_DEBUG = -g
MACH_OPT_HIGH = -O2
MACH_OPT_AGGRESSIVE = -O3 -g

#-----------------------------------------------------------------------
# Includes
#-----------------------------------------------------------------------

LOCAL_INCLUDES_HDF5 = -I$(LOCAL_HDF5_INSTALL)/include # HDF5 includes

MACH_INCLUDES = $(LOCAL_INCLUDES_HDF5)

#-----------------------------------------------------------------------
# Libraries
#-----------------------------------------------------------------------

LOCAL_LIBS_HDF5 = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 -lz # HDF5 libraries
LOCAL_LIBS_MACH = -lgfortran # Machine-dependent libraries

MACH_LIBS = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)

#-----------------------------------------------------------------------
# Installation
#-----------------------------------------------------------------------

MACH_INSTALL_PREFIX = $(HOME)/usr/local
MACH_INSTALL_LIB_DIR =
MACH_INSTALL_INCLUDE_DIR =
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