diff --git a/moose-core/.travis.yml b/moose-core/.travis.yml
index 7a134ba7fc4a69d462617c4e22315e601ab2edfb..6c3cd42eeb7af56690f9a640b197f9130b42b9d1 100644
--- a/moose-core/.travis.yml
+++ b/moose-core/.travis.yml
@@ -1,6 +1,8 @@
language: cpp
dist: trusty
sudo: required
+group: edge
+
compiler:
- gcc
- clang
diff --git a/moose-core/CONTRIBUTING.md b/moose-core/CONTRIBUTING.md
new file mode 100644
index 0000000000000000000000000000000000000000..f9abad879e039b284f91425052c7bc7781477059
--- /dev/null
+++ b/moose-core/CONTRIBUTING.md
@@ -0,0 +1,5 @@
+To contribute, fork this repo and submit your changes via a pull-request.
+Before sending pull-request, check the following:
+
+- [ ] Software builds locally
+- [ ] `ctest --output-on-failure` passes all tests.
diff --git a/moose-core/Makefile b/moose-core/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..5dda459827e9ab9c719b762b9e19946bd0ab0daf
--- /dev/null
+++ b/moose-core/Makefile
@@ -0,0 +1,512 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment,
+#** also known as GENESIS 3 base code.
+#** copyright (C) 2003- 2006 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+#######################################################################
+# NOTE:
+# This Makefile is compatible with _GNU Make_.
+# This does not work with nmake or borland make.
+# You may have to specify some variables when calling gnu make as
+# described in the comments below. The defaults should work on most
+# Unix clones.
+########################################################################
+
+# Linux compilation:
+# We recommend two levels of compilation: either full debug, with gdb,
+# unit tests and all the rest, or an optimized version for production
+# simulations, without any unit tests or assertions. If you want some
+# intermediate levels, edit the flags.
+######################################################################
+#
+# ADDITIONAL COMMANDLINE VARIABLES FOR MAKE
+#
+######################################################################
+# The variable BUILD determines if it should be optimized (release)
+# or a debug version (default).
+# make can be run with a command line parameter like below:
+# make clean BUILD=debug
+# make BUILD=debug
+# another option is to define BUILD as an environment variable:
+# export BUILD=debug
+# make clean
+# make
+#
+# There are some more variables which just need to be defined for
+# controlling the compilation and the value does not matter. These are:
+#
+# USE_GSL - use GNU Scientific Library for integration in kinetic simulations
+#
+# USE_READLINE - use the readline library which provides command history and
+# better command line editing capabilities
+#
+# GENERATE_WRAPPERS - useful for python interface developers. The binary created
+# with this option looks for a directory named 'generated' in the
+# working directory and creates a wrapper class ( one .h file
+# and a .cpp file ) and partial code for the swig interface file
+# (pymoose.i). These files with some modification can be used for
+# generating the python interface using swig.
+#
+# USE_MPI - compile with support for parallel computing through MPICH library
+
+
+# Default values for flags. The operator ?= assigns the given value only if the
+# variable is not already defined.
+
+USE_HDF5?=1
+USE_CUDA?=0
+USE_NEUROKIT?=0
+PYTHON?=2
+# BUILD (= debug, release)
+ifndef BUILD
+BUILD=release
+endif
+
+#If using mac uncomment the following lines
+# PLATFORM=mac
+#export PLATFORM
+
+# Get the processor architecture - i686 or x86_64
+# All these should be taken care of in a script, not in the
+# Makefile. But we are
+ifndef MACHINE
+MACHINE=i686
+endif
+# We are assuming all non-win32 systems to be POSIX compliant
+# and thus have the command uname for getting Unix system name
+ifneq ($(OSTYPE),win32)
+MACHINE=$(shell uname -m)
+PLATFORM := $(shell uname -s)
+endif
+
+USE_NUMPY=1
+# Debug mode:
+
+ifeq ($(BUILD),debug)
+CXXFLAGS = -g -O0 -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
+USE_GSL = true
+endif
+# Optimized mode:
+ifeq ($(BUILD),release)
+CXXFLAGS = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
+USE_GSL = true
+endif
+# Profiling mode:
+ifeq ($(BUILD),profile)
+CXXFLAGS = -O3 -pg -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
+USE_GSL = true
+endif
+# Profiling mode with gperftoools
+ifeq ($(BUILD),gperf)
+CXXFLAGS = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
+LDFLAGS += -lprofiler -ltcmalloc
+USE_GSL = true
+endif
+# Threading mode:
+ifeq ($(BUILD),thread)
+CXXFLAGS = -O3 -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
+USE_GSL = true
+endif
+
+# MPI mode:
+ifeq ($(BUILD),mpi)
+CXXFLAGS = -g -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
+USE_MPI = 1
+USE_GSL = true
+endif
+
+# optimized MPI mode:
+ifeq ($(BUILD),ompi)
+CXXFLAGS = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
+USE_MPI = 1
+USE_GSL = true
+endif
+
+# optimised mode but with unit tests.
+ifeq ($(BUILD),odebug)
+CXXFLAGS = -O3 -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
+USE_GSL = true
+endif
+
+# including SMOLDYN
+ifdef USE_SMOLDYN
+CXXFLAGS = -g -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
+USE_GSL = true
+endif
+
+# Use a strict compilation
+ifeq ($(BUILD),developer)
+ CXXFLAGS=-g \
+ -Wall -Werror -Wno-unused-variable -Wno-unused-function \
+ -DDO_UNIT_TESTS -DDEVELOPER -DDEBUG
+ USE_GSL = true
+endif
+##########################################################################
+#
+# MAC OS X compilation, Debug mode:
+ifeq ($(PLATFORM),Darwin)
+CXXFLAGS += -DMACOSX # GCC compiler also sets __APPLE__ for Mac OS X which can be used instead
+CXXFLAGS += -Wno-deprecated -force_cpusubtype_ALL -mmacosx-version-min=10.4
+endif
+# Use the options below for compiling on GCC4.1
+# GNU C++ 4.1 and newer might need -ffriend-injection
+#
+#CXXFLAGS = -g -Wall -pedantic -DDO_UNIT_TESTS -ffriend-injection -DUSE_GENESIS_PARSER
+
+# Insert the svn revision no. into the code as a preprocessor macro.
+# Only for release versions we want to pass SVN=0 to make.
+# No more SVN so pass zero
+SVN=0
+ifndef SVN
+SVN?=1
+endif
+empty :=
+space := $(empty) $(empty)
+ifneq ($(SVN),0)
+# Some versions of svnrevision return "Unversioned directory" which causes confusion to gcc
+SVN_REVISION := $(shell svnversion)
+SVN_REVISION := $(subst $(space),_,$(SVN_REVISION))
+# SVN_REVISION := $(subst :,_,$(SVN_REVISION))
+ifneq ($(SVN_REVISION),export)
+CXXFLAGS+=-DSVN_REVISION=\"$(SVN_REVISION)\"
+endif
+endif
+
+
+# Libraries are defined below.
+SUBLIBS =
+# Notice that pthread is no more included
+LIBS = -L/usr/lib -L/usr/local/lib
+
+#LIBS = -lm
+
+# For 64 bit Linux systems add paths to 64 bit libraries
+ifeq ($(PLATFORM),Linux)
+CXXFLAGS += -DLINUX
+ifeq ($(MACHINE),x86_64)
+LIBS+= -L/lib64 -L/usr/lib64
+endif
+endif
+
+##########################################################################
+#
+# Developer options (Don't try these unless you are writing new code!)
+##########################################################################
+# For parallel (MPI) version:
+ifdef USE_MUSIC
+USE_MPI = 1 # Automatically enable MPI if USE_MUSIC is on
+CXXFLAGS += -DUSE_MUSIC
+LIBS += -lmusic
+endif
+
+# The -DMPICH_IGNORE_CXX_SEEK flag is because of a bug in the
+# MPI-2 standard. Enabled by default because it use crops up
+# often enough. You won't need if if you are not using MPICH, or
+# if your version of MPICH has fixed the issue.
+ifdef USE_MPI
+# CXXFLAGS += -DUSE_MPI
+CXXFLAGS += -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK
+endif
+
+#use this for readline library
+#CXXFLAGS = -g -Wall -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DUSE_READLINE
+
+
+# To use GSL, pass USE_GSL=true ( anything on the right will do) in make command line
+ifdef USE_GSL
+LIBS+= $(shell gsl-config --libs)
+#LIBS+= -L/usr/lib -Wl,--no-as-needed -lgsl -lgslcblas -lm
+#LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
+CXXFLAGS+= -DUSE_GSL
+else
+LIBS+= -lm
+endif
+
+#Saeed
+# To use CUDA, pass USE_CUDA=1 in make command line
+ifeq ($(USE_CUDA),1)
+LIBS+= -L/usr/local/cuda/lib64 -LhsolveCuda/cudaLibrary -lcuda -lcudart -lm -lmooseCudaLibrary
+HCUDA_DIR = hsolveCuda
+HCUDA_LIB = hsolveCuda/_hsolveCuda.o
+endif
+
+# To disable numpy pass USE_NUMPY=0
+ifeq ($(USE_NUMPY),1)
+CXXFLAGS+=-DUSE_NUMPY
+endif
+
+# To compile examples, pass EXAMPLES=true ( anything on the right will do) in make command line
+ifdef EXAMPLES
+EXAMPLES_DIR = examples
+EXAMPLES_LIB = examples/_trials.o
+endif
+
+# To use Smoldyn, pass USE_SMOLDYN=true ( anything on the right will do) in make command line
+ifdef USE_SMOLDYN
+#LIBS+= -L/usr/local/lib -lsmoldyn
+CXXFLAGS+= -DUSE_SMOLDYN
+SMOLDYN_DIR = smol
+SMOLDYN_LIB = smol/_smol.o /usr/local/lib/libsmoldyn.a
+LIBS += -lsmoldyn
+endif
+
+# To compile with readline support pass USE_READLINE=true in make command line
+ifdef USE_READLINE
+LIBS+= -lreadline
+CXXFLAGS+= -DUSE_READLINE
+endif
+
+# To compile with curses support (terminal aware printing) pass USE_CURSES=true in make command line
+ifdef USE_CURSES
+LIBS += -lcurses
+CXXFLAGS+= -DUSE_CURSES
+endif
+
+ifdef USE_MUSIC
+ MUSIC_DIR = music
+ MUSIC_LIB = music/music.o
+endif
+
+# Here we automagically change compilers to deal with MPI.
+ifdef USE_MPI
+ CXX = mpicxx
+# CXX = /usr/local/mvapich2/bin/mpicxx
+# PARALLEL_DIR = parallel
+# PARALLEL_LIB = parallel/parallel.o
+else
+ CXX = g++
+# CXX = CC # Choose between Solaris CC and g++ on a Solaris machine
+endif
+
+ifeq ($(USE_HDF5),1)
+ CXXFLAGS+= -DUSE_HDF5 -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include -I/usr/include/hdf5/serial
+ LIBS+= -lhdf5 -lhdf5_hl -L/usr/local/hdf5/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial/
+endif
+
+LD = ld
+
+SUBDIR = \
+ basecode \
+ msg \
+ shell \
+ randnum\
+ scheduling\
+ mpi \
+ builtins\
+ utility \
+ external/muparser \
+ biophysics \
+ synapse \
+ intfire \
+ kinetics \
+ ksolve \
+ mesh \
+ hsolve \
+ diffusion \
+ device \
+ signeur \
+ benchmarks \
+ $(SMOLDYN_DIR) \
+ $(SBML_DIR) \
+ $(HCUDA_DIR) \
+ $(EXAMPLES_DIR) \
+
+# Used for 'make clean'
+CLEANSUBDIR = $(SUBDIR) $(PARALLEL_DIR) pymoose
+
+OBJLIBS = \
+ basecode/_basecode.o \
+ msg/_msg.o \
+ shell/_shell.o \
+ randnum/_randnum.o \
+ scheduling/_scheduling.o \
+ mpi/_mpi.o \
+ builtins/_builtins.o \
+ utility/_utility.o \
+ external/muparser/_muparser.o \
+ biophysics/_biophysics.o \
+ synapse/_synapse.o \
+ intfire/_intfire.o \
+ kinetics/_kinetics.o \
+ ksolve/_ksolve.o \
+ hsolve/_hsolve.o \
+ mesh/_mesh.o \
+ diffusion/_diffusion.o \
+ device/_device.o \
+ signeur/_signeur.o \
+ benchmarks/_benchmarks.o \
+ $(SMOLDYN_LIB) \
+ $(SBML_LIB) \
+ $(HCUDA_LIB) \
+ $(EXAMPLES_LIB) \
+
+
+ifeq ($(USE_NEUROKIT),1)
+ NEUROKIT_COMMAND = cd ./python/moogli; python setup.py build; cd ../../; cp ./python/moogli/build/*/_moogli.so ./python/moogli/;
+# else
+# NEUROKIT_COMMAND = ""
+endif
+
+
+export CXX
+export CXXFLAGS
+export LD
+export LIBS
+export USE_GSL
+#export USE_SBML
+
+all: moose pymoose
+
+neurokit: ./python/moogli/setup.py
+ $(NEUROKIT_COMMAND)
+
+moose: libs $(OBJLIBS) $(PARALLEL_LIB)
+ $(CXX) $(CXXFLAGS) $(OBJLIBS) $(PARALLEL_LIB) $(LIBS) -o moose
+ @echo "Moose compilation finished"
+
+libmoose.so: libs
+ $(CXX) -G $(LIBS) -o libmoose.so
+ @echo "Created dynamic library"
+
+# Get the python version
+ifneq ($(OSTYPE),win32)
+ifeq ($(PYTHON),3)
+PYTHON_VERSION := $(subst ., ,$(lastword $(shell python3 --version 2>&1)))
+PYTHON_CFLAGS := $(shell python3-config --cflags)
+PYTHON_LDFLAGS := $(shell python3-config --ldflags)
+else # Python 2.x
+PYTHON_VERSION := $(subst ., ,$(lastword $(shell python --version 2>&1)))
+ifneq ($(BUILD),debug)
+PYTHON_CFLAGS := $(shell python-config --cflags)
+PYTHON_LDFLAGS := $(shell python-config --ldflags)
+else
+PYTHON_CFLAGS := $(shell python-config --includes) \
+ -fno-strict-aliasing -fwrapv \
+ -Wstrict-prototypes \
+ -Wformat -Wformat-security -Werror=format-security \
+ -fstack-protector --param=ssp-buffer-size=4
+
+PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON) \
+ -Xlinker -export-dynamic -Wl,-O0 -Wl,-Bsymbolic-functions
+endif # ifneq ($(BUILD),debug)
+endif # ifeq ($(PYTHON),3)
+PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION})
+PYTHON_VERSION_MINOR := $(word 2,${PYTHON_VERSION})
+INSTALLED_PYTHON := python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
+endif
+
+# For developer build and strict checking
+ifeq ($(BUILD),developer)
+ PYTHON_CFLAGS := $(PYTHON_CFLAGS) -Wall -Werror -Wno-unused-function -Wno-unused-variable
+endif # ifeq(${BUILD},developer)
+
+ifndef PYTHON_CFLAGS
+PYTHON_CFLAGS := -I/usr/include/$(INSTALLED_PYTHON) -fno-strict-aliasing \
+ -fwrapv \
+ -fstack-protector \
+ #-Wstrict-prototypes \ # This option is obsolete for g++-4.8
+ --param=ssp-buffer-size=4 \
+ -Wformat -Wformat-security -Werror=format-security
+
+PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON) -Xlinker -export-dynamic -Wl,-O0 -Wl,-Bsymbolic-functions
+endif
+# There are some unix/gcc specific paths here. Should be cleaned up in future.
+pymoose: python/moose/_moose.so
+pymoose: CXXFLAGS += -DPYMOOSE $(PYTHON_CFLAGS)
+# fix: add include dir for numpy headers required by pymoose/moosemodule.cpp
+pymoose: CXXFLAGS += -I$(shell /usr/bin/python -c 'from numpy import get_include; print get_include()')
+pymoose: OBJLIBS += pymoose/_pymoose.o
+pymoose: LDFLAGS += $(PYTHON_LDFLAGS)
+export CXXFLAGS
+python/moose/_moose.so: libs $(OBJLIBS)
+ $(MAKE) -C pymoose
+ $(CXX) -shared $(LDFLAGS) $(CXXFLAGS) -o $@ $(OBJLIBS) $(LIBS)
+ @echo "pymoose module built."
+
+# This will generate an object file without main
+libs:
+ @for i in $(SUBDIR) $(PARALLEL_DIR); do \
+ $(MAKE) -C $$i || exit $$?; \
+ done
+ @echo "All Libs compiled"
+
+clean:
+ @(for i in $(CLEANSUBDIR) ; do $(MAKE) -C $$i clean; done)
+ -rm -rf moose core.* DOCS/html python/moose/*.so python/moose/*.pyc
+
+############ INSTALL (works for sudo make install and deb packaging using dpkg-buildpackage)
+## get the default python module install location
+## no need to know this, the default for public modules is /usr/share/pyshared
+pydir_cmd := python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"
+pydistpkg_dir := $(shell $(pydir_cmd))
+## /usr/share/pyshared/ is a directory which is independent of python version,
+## but modules need to be registered with update-python-modules, giving a list of files
+## debhelper (dpkg-buildpackage) will also copy to this location and do the registration.
+## For make install, I stick to the default python .../dist-packages directory.
+pydistpkg_dirB := /usr/share/pyshared/
+
+username=$(shell basename $(HOME))
+
+install_prefix=/usr
+## Note that $(DESTDIR) is provided by dpkg-buildpackage to specify the local install for deb packaging
+## if doing sudo make install, $(DESTDIR) will be undefined and will cause no trouble
+install:
+ ## discard symbols from object files
+ strip python/moose/_moose.so
+
+ ## delete older .../share/moose, - before rm means ignore errors (eg not found)
+ -rm -rf $(DESTDIR)$(install_prefix)/share/moose
+ ## -p creates parent directories also if they don't exist
+ mkdir -p $(DESTDIR)$(install_prefix)/share/moose
+ ## copy filtering out the .svn (hidden) files
+ rsync -r --exclude=.svn Demos/* $(DESTDIR)$(install_prefix)/share/moose/Demos
+ rsync -r --exclude=.svn gui/* $(DESTDIR)$(install_prefix)/share/moose/gui
+ test -d $(DESTDIR)$(install_prefix)/share/doc || mkdir -p $(DESTDIR)$(install_prefix)/share/doc
+ rsync -r --exclude=.svn Docs/* $(DESTDIR)$(install_prefix)/share/doc/moose
+ # rsync -r --exclude=.svn Demos/* $(DESTDIR)$(install_prefix)/share/moose/
+ ## pymoose module goes to python's dist-packages
+ ## delete older .../dist-packages/moose, - before rm means ignore errors (eg not found)
+ -rm -rf $(DESTDIR)$(pydistpkg_dir)/moose
+ -rm -rf $(DESTDIR)$(pydistpkg_dirB)/moose
+ ## make directory in case non-existent (needed for deb pkg building)
+ mkdir -p $(DESTDIR)$(pydistpkg_dir)
+ rsync -r --exclude=.svn --exclude=moose_py3k.py python/* $(DESTDIR)$(pydistpkg_dir)/
+
+ ## shell command moosegui for the moose GUI.
+ chmod a+x $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py
+ ## -rm instructs make to ignore errors from make eg. file not found
+ -rm -f $(DESTDIR)$(install_prefix)/bin/moosegui
+ mkdir -p $(DESTDIR)$(install_prefix)/bin
+ ln -s $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py $(DESTDIR)$(install_prefix)/bin/moosegui
+
+ ## byte compile the module, gui, Demos (since, later running as user cannot create .pyc in root-owned dirs)
+ python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(pydistpkg_dir)/moose',force=1)"
+ python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(install_prefix)/share/moose/gui',force=1)"
+ python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(install_prefix)/share/moose/Demos',force=1)"
+
+ ## see standards.freedesktop.org for specifications for where to put menu entries and icons
+ ## copy the .desktop files to /usr/share/applications for link to show up in main menu
+ mkdir -p $(DESTDIR)$(install_prefix)/share/applications
+ cp gui/MooseGUI.desktop $(DESTDIR)$(install_prefix)/share/applications/
+ cp gui/MooseSquidAxon.desktop $(DESTDIR)$(install_prefix)/share/applications/
+ ## copy the .desktop files to the desktop too to get icons
+ cp gui/MooseGUI.desktop $$HOME/Desktop/
+ chmod a+x $$HOME/Desktop/MooseGUI.desktop
+ chown $(username) $(HOME)/Desktop/MooseGUI.desktop
+ chgrp $(username) $(HOME)/Desktop/MooseGUI.desktop
+ cp gui/MooseSquidAxon.desktop $$HOME/Desktop/
+ chmod a+x $$HOME/Desktop/MooseSquidAxon.desktop
+ chgrp $(username) $(HOME)/Desktop/MooseSquidAxon.desktop
+ chown $(username) $(HOME)/Desktop/MooseSquidAxon.desktop
+ ## copy icon to /usr/share/icons/hicolor/<size>/apps (hicolor is the fallback theme)
+ mkdir -p $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps
+ cp gui/icons/moose_icon.png $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps/
+ cp gui/icons/squid.png $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps/
+ ## need to update the icon cache to show the icon
+ update-icon-caches $(DESTDIR)$(install_prefix)/share/icons/hicolor/
+
+.PHONY: install
diff --git a/moose-core/basecode/Makefile b/moose-core/basecode/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..0639a32c38bce0311fda0e32251dbd5b44eab69a
--- /dev/null
+++ b/moose-core/basecode/Makefile
@@ -0,0 +1,99 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment,
+#** also known as GENESIS 3 base code.
+#** copyright (C) 2004 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+# $Id: $
+#
+# $Log: $
+#
+
+TARGET = _basecode.o
+
+
+# CXXFLAGS += -I.. -I../kinetics -I../biophysics
+
+OBJ = \
+ consts.o \
+ Element.o \
+ DataElement.o \
+ GlobalDataElement.o \
+ LocalDataElement.o \
+ Eref.o \
+ Finfo.o \
+ DestFinfo.o \
+ Cinfo.o \
+ SrcFinfo.o \
+ ValueFinfo.o \
+ SharedFinfo.o \
+ FieldElementFinfo.o \
+ FieldElement.o \
+ Id.o \
+ ObjId.o \
+ global.o \
+ SetGet.o \
+ OpFuncBase.o \
+ EpFunc.o \
+ HopFunc.o \
+ SparseMatrix.o \
+ doubleEq.o \
+ testAsync.o \
+ main.o \
+
+HEADERS = \
+ header.h \
+ Cinfo.h \
+ Conv.h \
+ Dinfo.h \
+ MsgDigest.h \
+ Element.h \
+ DataElement.h \
+ GlobalDataElement.h \
+ LocalDataElement.h \
+ Eref.h \
+ global.h \
+ Finfo.h \
+ DestFinfo.h \
+ Id.h \
+ ObjId.h \
+ ../msg/Msg.h \
+ OpFuncBase.h \
+ OpFunc.h \
+ EpFunc.h \
+ HopFunc.h \
+ ProcInfo.h \
+ SrcFinfo.h \
+ ValueFinfo.h \
+ LookupValueFinfo.h \
+ LookupElementValueFinfo.h \
+ SharedFinfo.h \
+ FieldElementFinfo.h \
+ FieldElement.h \
+ MsgFuncBinding.h \
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS) ../shell/Shell.h
+Element.o: FuncOrder.h
+testAsync.o: SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynEvent.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h ../randnum/RNG.h
+SparseMsg.o: SparseMatrix.h
+SetGet.o: SetGet.h ../shell/Neutral.h
+HopFunc.o: HopFunc.h ../mpi/PostMaster.h
+global.o: global.h ../randnum/RNG.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) -I../msg -I.. $< -c
+
+.PHONY: pymoose
+
+pymoose: CXXFLAGS += -DPYMOOSE
+
+$(TARGET): $(OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/benchmarks/Makefile b/moose-core/benchmarks/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..0eb5aef3628e1e1c1d3186dab04ebbb7b861de48
--- /dev/null
+++ b/moose-core/benchmarks/Makefile
@@ -0,0 +1,31 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _benchmarks.o
+
+OBJ = \
+ benchmarks.o \
+ kineticMarks.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+kineticMarks.o: ../shell/Shell.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/biophysics/Makefile b/moose-core/biophysics/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..6659630cea1751622c725f27a6a9142bf277384f
--- /dev/null
+++ b/moose-core/biophysics/Makefile
@@ -0,0 +1,123 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _biophysics.o
+
+OBJ = \
+ IntFire.o \
+ SpikeGen.o \
+ RandSpike.o \
+ CompartmentDataHolder.o \
+ CompartmentBase.o \
+ Compartment.o \
+ SymCompartment.o \
+ GapJunction.o \
+ ChanBase.o \
+ ChanCommon.o \
+ HHChannelBase.o \
+ HHChannel.o \
+ HHGate.o \
+ HHGate2D.o \
+ HHChannel2D.o \
+ CaConcBase.o \
+ CaConc.o \
+ MgBlock.o \
+ Nernst.o \
+ Neuron.o \
+ Spine.o \
+ ReadCell.o \
+ SwcSegment.o \
+ ReadSwc.o \
+ SynChan.o \
+ NMDAChan.o \
+ testBiophysics.o \
+ IzhikevichNrn.o \
+ DifShellBase.o \
+ DifShell.o \
+ DifBufferBase.o \
+ DifBuffer.o \
+ Leakage.o \
+ VectorTable.o \
+ MarkovRateTable.o \
+ MarkovChannel.o \
+ MarkovGslSolver.o \
+ MatrixOps.o \
+ MarkovSolverBase.o \
+ MarkovSolver.o \
+ VClamp.o \
+
+
+ # MMpump.o \
+ # LeakyIaF.o \
+ # GapJunction.o \
+ # Nernst.o \
+ # GHK.o \
+ # NMDAChan.o \
+
+# GSL_LIBS = -L/usr/lib -lgsl
+
+HEADERS = \
+ ../basecode/header.h \
+ ../utility/numutil.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+IntFire.o: IntFire.h
+SpikeGen.o: SpikeGen.h
+RandSpike.o: RandSpike.h ../randnum/randnum.h
+CompartmentDataHolder.o: CompartmentDataHolder.h
+CompartmentBase.o: CompartmentBase.h CompartmentDataHolder.h
+Compartment.o: CompartmentBase.h Compartment.h
+SymCompartment.o: CompartmentBase.h Compartment.h SymCompartment.h
+ChanBase.o: ChanBase.h
+ChanCommon.o: ChanBase.h ChanCommon.h
+SynChan.o: SynChan.h ChanBase.h ChanCommon.h
+NMDAChan.o: NMDAChan.h SynChan.h ChanBase.h ChanCommon.h
+Leakage.o: Leakage.h ChanBase.h ChanCommon.h
+GapJunction.o: GapJunction.h
+HHChannelBase.o: ChanBase.h HHChannelBase.h HHGate.h
+HHChannel.o: ChanBase.h HHChannel.h HHGate.h
+HHGate.o: HHGate.h
+HHChannel2D.o: ChanBase.h HHChannel2D.h HHGate2D.h
+HHGate2D.o: HHGate2D.h
+CaConcBase.o: CaConcBase.h
+CaConc.o: CaConcBase.h CaConc.h
+MgBlock.o: MgBlock.h ChanBase.h
+Nernst.o: Nernst.h
+Neuron.o: Neuron.h SwcSegment.h Spine.h
+Spine.o: Neuron.h SwcSegment.h Spine.h
+ReadCell.o: CompartmentBase.h Compartment.h SymCompartment.h ReadCell.h ../shell/Shell.h ../utility/utility.h
+SwcSegment.o: SwcSegment.h ../utility/Vec.h
+ReadSwc.o: CompartmentBase.h Compartment.h SymCompartment.h SwcSegment.h ReadSwc.h ../shell/Shell.h ../utility/Vec.h
+IzhikevichNrn.o: IzhikevichNrn.h
+DifShellBase.o: DifShellBase.h
+DifShell.o: DifShellBase.h DifShell.h
+DifBufferBase.o: DifBufferBase.h
+DifBuffer.o: DifBufferBase.h DifBuffer.h
+MMPump.o: MMPump.h
+testBiophysics.o: IntFire.h CompartmentBase.h Compartment.h HHChannel.h HHGate.h
+VectorTable.o : VectorTable.h
+MarkovGslSolver.o : MarkovGslSolver.h
+MatrixOps.o : MatrixOps.h
+MarkovRateTable.o : VectorTable.h ../builtins/Interpol2D.h MarkovRateTable.h
+MarkovSolverBase.o : MarkovSolver.h MatrixOps.h MarkovRateTable.h
+MarkovSolver.o : MarkovSolverBase.h MarkovSolver.h
+MarkovChannel.o : VectorTable.h ../builtins/Interpol2D.h MarkovRateTable.h ChanBase.h MarkovChannel.h
+VClamp.o: VClamp.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../external/muparser/include -I .. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
+
+clean:
+ rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/biophysics/ReadSwc.cpp b/moose-core/biophysics/ReadSwc.cpp
index 6f6f5a2a3a9325533123cef054ee6302edf83585..9894e0472bf64628f75971fc76ae95f6d2c3ddf6 100644
--- a/moose-core/biophysics/ReadSwc.cpp
+++ b/moose-core/biophysics/ReadSwc.cpp
@@ -52,11 +52,7 @@ ReadSwc::ReadSwc( const string& fname )
cleanZeroLength();
parseBranches();
}
- if ( verbose || !valid || (badSegs > 0) )
- cout << "ReadSwc: " << fname <<
- " : " << (valid ? "OK" : "FAILED" )<<
- ", # Branches = " << branches_.size() <<
- ". # Segs = " << segs_.size() <<
+ cout << "ReadSwc: " << fname << " : NumSegs = " << segs_.size() <<
", bad = " << badSegs <<
", Validated = " << valid <<
", numBranches = " << branches_.size() <<
diff --git a/moose-core/builtins/Makefile b/moose-core/builtins/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..7ff1cebed8784468dcd0aec5a15ea65db4f1220f
--- /dev/null
+++ b/moose-core/builtins/Makefile
@@ -0,0 +1,68 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _builtins.o
+
+OBJ = \
+ Arith.o \
+ Group.o \
+ Mstring.o \
+ Func.o \
+ Function.o \
+ Variable.o \
+ InputVariable.o \
+ TableBase.o \
+ Table.o \
+ Interpol.o \
+ StimulusTable.o \
+ TimeTable.o \
+ Stats.o \
+ SpikeStats.o \
+ Interpol2D.o \
+ HDF5WriterBase.o \
+ HDF5DataWriter.o \
+ StreamerBase.o \
+ Streamer.o \
+ NSDFWriter.o \
+ testNSDF.o \
+ testBuiltins.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+Arith.o: Arith.h
+Group.o: Group.h
+Mstring.o: Mstring.h
+Func.o: Func.h
+Function.o: Function.h
+Variable.o: Variable.h
+TableBase.o: TableBase.h
+Table.o: TableBase.h Table.h
+Interpol.o: TableBase.h Interpol.h
+StimulusTable.o: TableBase.h StimulusTable.h
+TimeTable.o: TimeTable.h TableBase.h
+Stats.o: Stats.h
+SpikeStats.o: Stats.h SpikeStats.h
+Interpol2D.o: Interpol2D.h
+HDF5WriterBase.o: HDF5WriterBase.h
+HDF5DataWriter.o: HDF5DataWriter.h HDF5WriterBase.h
+testBuiltins.o: Group.h Arith.h Stats.h ../msg/DiagonalMsg.h ../basecode/SetGet.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../scheduling -I../basecode -I../msg -I../external/muparser/include $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/device/Makefile b/moose-core/device/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..159d88056dade350936d92f016e3221df7d2e321
--- /dev/null
+++ b/moose-core/device/Makefile
@@ -0,0 +1,26 @@
+TARGET = _device.o
+
+OBJ = PulseGen.o \
+ DiffAmp.o \
+ PIDController.o \
+ RC.o
+
+HEADERS = \
+ ../basecode/header.h \
+
+default: $(TARGET)
+
+$(OBJ): $(HEADERS)
+PulseGen.o: PulseGen.h
+DiffAmp.o: DiffAmp.h
+PIDController.o: PIDController.h
+RC.o: RC.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
+
+clean:
+ rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/diffusion/Makefile b/moose-core/diffusion/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..458a5ba9e8026e4675a8e9b2ce525da713047389
--- /dev/null
+++ b/moose-core/diffusion/Makefile
@@ -0,0 +1,36 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _diffusion.o
+
+OBJ = \
+ FastMatrixElim.o \
+ DiffPoolVec.o \
+ Dsolve.o \
+ testDiffusion.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+FastMatrixElim.o: ../basecode/SparseMatrix.h FastMatrixElim.h
+Dsolve.o: ../basecode/SparseMatrix.h ../kinetics/PoolBase.h ../kinetics/lookupVolumeFromMesh.h ../mesh/ChemCompt.h ../ksolve/XferInfo.h ../ksolve/ZombiePoolInterface.h
+DiffPoolVec.o: DiffPoolVec.h ../ksolve/ZombiePoolInterface.h
+testDiffusion.o: Dsolve.h ../ksolve/ZombiePoolInterface.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(GSL_FLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../ksolve $< -c
+
+$(TARGET): $(OBJ) $(GSL_OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(GSL_OBJ) $(GSL_LIBS) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/examples/Makefile b/moose-core/examples/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..1e7f10aba87a81427787ebda1f04f6ab3a10f31b
--- /dev/null
+++ b/moose-core/examples/Makefile
@@ -0,0 +1,32 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _trials.o
+
+OBJ = \
+ Example.o \
+ Ex.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+Example.o: Example.h ../basecode/ElementValueFinfo.h
+Ex.o: Ex.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/external/muparser/Makefile b/moose-core/external/muparser/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..6b8bb423a78aec4c2840cea4ff9d2181a6bdffb4
--- /dev/null
+++ b/moose-core/external/muparser/Makefile
@@ -0,0 +1,42 @@
+# Makefile for including muParser into moose.
+# Author: Subhasis Ray
+#
+TARGET = _muparser.o
+
+OBJ = \
+ src/muParserBase.o \
+ src/muParserBytecode.o \
+ src/muParserCallback.o \
+ src/muParser.o \
+ src/muParserDLL.o \
+ src/muParserError.o \
+ src/muParserInt.o \
+ src/muParserTokenReader.o \
+
+HEADERS = \
+ include/muParser.h \
+ include/muParserBase.h \
+ include/muParserBytecode.h \
+ include/muParserCallback.h \
+ include/muParserDef.h \
+ include/muParserError.h \
+ include/muParserFixes.h \
+ include/muParserStack.h \
+ include/muParserToken.h \
+ include/muParserTokenReader.h \
+ include/muParserTemplateMagic.h \
+
+
+default: $(TARGET)
+
+$(OBJ): $(HEADERS)
+
+%.o: %.cpp
+ $(CXX) $(CXXFLAGS) -I. -I../../ -Iinclude $< -c -o $@
+
+$(TARGET): $(OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
+
diff --git a/moose-core/external/tinyxml/Makefile b/moose-core/external/tinyxml/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..45639837dea61df6d90bf23b3e5a7ee081d3a4d3
--- /dev/null
+++ b/moose-core/external/tinyxml/Makefile
@@ -0,0 +1,25 @@
+# Makefile for including muParser into moose.
+# Author: Subhasis Ray
+#
+TARGET = _tinyxml2.o
+
+OBJ = \
+ tinyxml2.o
+
+HEADERS = \
+ tinyxml2.h \
+
+
+default: $(TARGET)
+
+$(OBJ): $(HEADERS)
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) -I. $< -c
+
+$(TARGET): $(OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
+
diff --git a/moose-core/hsolve/Makefile b/moose-core/hsolve/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..da4e33a3a96c04e163d07ea2c2c454f08f9787cd
--- /dev/null
+++ b/moose-core/hsolve/Makefile
@@ -0,0 +1,52 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment,
+#** also known as GENESIS 3 base code.
+#** copyright (C) 2004 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU General Public License version 2
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _hsolve.o
+
+OBJ = \
+ HSolveStruct.o \
+ HinesMatrix.o \
+ HSolvePassive.o \
+ RateLookup.o \
+ HSolveActive.o \
+ HSolveActiveSetup.o \
+ HSolveInterface.o \
+ HSolve.o \
+ HSolveUtils.o \
+ testHSolve.o \
+ ZombieCompartment.o \
+ ZombieCaConc.o \
+ ZombieHHChannel.o \
+
+HEADERS = \
+ ../basecode/header.h
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+HSolveStruct.o: HSolveStruct.h
+HinesMatrix.o: HinesMatrix.h TestHSolve.h
+HSolvePassive.o: HSolvePassive.h HinesMatrix.h HSolveStruct.h HSolveUtils.h TestHSolve.h ../biophysics/Compartment.h
+RateLookup.o: RateLookup.h
+HSolveActive.o: HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h
+HSolveActiveSetup.o: HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h HSolveUtils.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHGate.h ../biophysics/CaConc.h
+HSolveInterface.o: HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h
+HSolve.o: ../biophysics/Compartment.h ZombieCompartment.h ../biophysics/CaConc.h ZombieCaConc.h ../biophysics/HHGate.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ZombieHHChannel.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
+ZombieCompartment.o: ../biophysics/CompartmentBase.h ZombieCompartment.h ../biophysics/Compartment.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
+ZombieCaConc.o: ZombieCaConc.h ../biophysics/CaConc.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
+ZombieHHChannel.o: ZombieHHChannel.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHGate.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
+
+clean:
+ rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/intfire/Makefile b/moose-core/intfire/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..22261ff9da1a87687e980907a90c5b0172697c0d
--- /dev/null
+++ b/moose-core/intfire/Makefile
@@ -0,0 +1,50 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _intfire.o
+
+OBJ = \
+ IntFireBase.o \
+ LIF.o \
+ QIF.o \
+ ExIF.o \
+ AdExIF.o \
+ AdThreshIF.o \
+ IzhIF.o \
+ testIntFire.o \
+
+# GSL_LIBS = -L/usr/lib -lgsl
+
+HEADERS = \
+ ../basecode/header.h \
+ ../utility/numutil.h \
+ IntFireBase.h \
+ ../biophysics/CompartmentBase.h \
+ ../biophysics/Compartment.h
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+LIF.o: LIF.h
+QIF.o: QIF.h
+ExIF.o: ExIF.h
+AdExIF.o: AdExIF.h
+AdThreshIF.o: AdThreshIF.h
+IzhIF.o: IzhIF.h
+testIntFire.o: LIF.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
+
+clean:
+ rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/kinetics/Makefile b/moose-core/kinetics/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..9b1f6375d239b8b1ad2ba39eaac061ad0db25d7f
--- /dev/null
+++ b/moose-core/kinetics/Makefile
@@ -0,0 +1,58 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _kinetics.o
+
+OBJ = \
+ PoolBase.o \
+ Pool.o \
+ BufPool.o \
+ ReacBase.o \
+ Reac.o \
+ EnzBase.o \
+ CplxEnzBase.o \
+ Enz.o \
+ MMenz.o \
+ Species.o \
+ ReadKkit.o \
+ WriteKkit.o \
+ ReadCspace.o \
+ lookupVolumeFromMesh.o \
+ testKinetics.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+Pool.o: PoolBase.h Pool.h lookupVolumeFromMesh.h
+BufPool.o: PoolBase.h Pool.h BufPool.h lookupVolumeFromMesh.h
+ReacBase.o: ReacBase.h lookupVolumeFromMesh.h
+Reac.o: ReacBase.h Reac.h lookupVolumeFromMesh.h
+EnzBase.o: EnzBase.h lookupVolumeFromMesh.h
+CplxEnzBase.o: EnzBase.h CplxEnzBase.h lookupVolumeFromMesh.h
+Enz.o: EnzBase.h CplxEnzBase.h Enz.h lookupVolumeFromMesh.h
+MMenz.o: EnzBase.h MMenz.h lookupVolumeFromMesh.h
+Boundary.o: Boundary.h
+Species.o: Species.h
+ReadKkit.o: lookupVolumeFromMesh.h ReadKkit.h PoolBase.h Pool.h ../shell/Shell.h
+WriteKkit.o: lookupVolumeFromMesh.h PoolBase.h
+ReadCspace.o: lookupVolumeFromMesh.h ReadCspace.h ../shell/Shell.h
+lookupVolumeFromMesh.o: lookupVolumeFromMesh.h
+testKinetics.o: ReadKkit.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/ksolve/Makefile b/moose-core/ksolve/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..49b51df4a418ed42d20c7aa9c64bcd06d63c0806
--- /dev/null
+++ b/moose-core/ksolve/Makefile
@@ -0,0 +1,100 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _ksolve.o
+
+OBJ = \
+ KinSparseMatrix.o \
+ ZombiePool.o \
+ ZombieBufPool.o \
+ ZombieReac.o \
+ ZombieEnz.o \
+ ZombieMMenz.o \
+ ZombieFunction.o \
+ VoxelPoolsBase.o \
+ VoxelPools.o \
+ GssaVoxelPools.o \
+ RateTerm.o \
+ FuncTerm.o \
+ Stoich.o \
+ Ksolve.o \
+ SteadyStateGsl.o \
+ Gsolve.o \
+ ZombiePoolInterface.o \
+ testKsolve.o \
+
+HEADERS = \
+ ../basecode/header.h \
+ ../basecode/SparseMatrix.h \
+ ../basecode/ElementValueFinfo.h \
+ RateTerm.h \
+ ../external/muparser/include/muParser.h \
+ FuncTerm.h \
+ KinSparseMatrix.h \
+ XferInfo.h \
+ ZombiePoolInterface.h \
+ Stoich.h \
+ ../kinetics/Pool.h \
+ ../kinetics/lookupVolumeFromMesh.h \
+
+
+# The GSL library (GNU Scientific Library) provides a range of
+# numerical functions, which allow us to use various advanced integration
+# methods. The GslIntegrator accesses these. This library is licenced
+# under the GPL, so only GPL-compliant uses of MOOSE will be able to
+# use it. Should be fine for academic use.
+# Optional: Comment out the following three items if not using GSL
+ifeq ($(USE_GSL),1)
+GSL_OBJ = \
+
+
+GSL_LIBS = -L/usr/lib -lgsl -lgslcblas
+GSL_FLAGS = -DUSE_GSL
+endif
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+KinSparseMatrix.o: KinSparseMatrix.h ../basecode/SparseMatrix.h
+ZombiePool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ../kinetics/lookupVolumeFromMesh.h
+ZombieBufPool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ZombieBufPool.h ../kinetics/lookupVolumeFromMesh.h
+ZombieBufPool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h
+VoxelPoolsBase.o: VoxelPoolsBase.h ../randnum/RNG.h
+VoxelPools.o: VoxelPoolsBase.h VoxelPools.h OdeSystem.h RateTerm.h Stoich.h
+GssaVoxelPools.o: VoxelPoolsBase.h GssaVoxelPools.h ../basecode/SparseMatrix.h \
+ ../randnum/RNG.h KinSparseMatrix.h GssaSystem.h RateTerm.h Stoich.h
+RateTerm.o: RateTerm.h
+FuncTerm.o: FuncTerm.h
+Stoich.o: RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h ../kinetics/PoolBase.h ../kinetics/ReacBase.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../basecode/SparseMatrix.h KinSparseMatrix.h ../scheduling/Clock.h ZombiePoolInterface.h
+ZombieReac.o: RateTerm.h FuncTerm.h Stoich.h ../kinetics/ReacBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieReac.h
+ZombieEnz.o: RateTerm.h FuncTerm.h Stoich.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieEnz.h
+ZombieMMenz.o: RateTerm.h FuncTerm.h Stoich.h ../kinetics/EnzBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieMMenz.h
+ZombieFunction.o: RateTerm.h FuncTerm.h Stoich.h ../builtins/Function.h ZombieFunction.h
+Ksolve.o: RateTerm.h Stoich.h Ksolve.h VoxelPoolsBase.h VoxelPools.h OdeSystem.h ZombiePoolInterface.h
+SteadyStateGsl.o: SteadyStateGsl.h ../basecode/SparseMatrix.h KinSparseMatrix.h RateTerm.h FuncTerm.h Stoich.h ../randnum/randnum.h
+Gsolve.o: RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h Gsolve.h VoxelPoolsBase.h VoxelPools.h GssaSystem.h ZombiePoolInterface.h ../basecode/SparseMatrix.h KinSparseMatrix.h
+ZombiePoolInterface.o: VoxelPoolsBase.h ZombiePoolInterface.h ../mesh/VoxelJunction.h Stoich.h ../shell/Shell.h
+testKsolve.o: ../shell/Shell.h
+
+#KineticHub.o: KineticHub.h
+
+ifeq ($(USE_GSL),1)
+#Optional: Comment out the following two items if not using GSL.
+$(GSL_OBJ) : $(HEADERS)
+#StateScanner.o: StateScanner.h
+endif # !USE_GSL
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(GSL_FLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg -I../kinetics -I../mesh -I../external/muparser/include -I../builtins $< -c
+
+$(TARGET): $(OBJ) $(GSL_OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(GSL_OBJ) $(GSL_LIBS) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/mesh/Makefile b/moose-core/mesh/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..9e211655654da3faa2c5d294e44000b7ddcde74a
--- /dev/null
+++ b/moose-core/mesh/Makefile
@@ -0,0 +1,55 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _mesh.o
+
+OBJ = \
+ ChemCompt.o \
+ MeshCompt.o \
+ MeshEntry.o \
+ CubeMesh.o \
+ CylBase.o \
+ CylMesh.o \
+ NeuroNode.o \
+ NeuroMesh.o \
+ SpineEntry.o \
+ SpineMesh.o \
+ PsdMesh.o \
+ testMesh.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+MeshEntry.o: MeshEntry.h
+Boundary.o: Boundary.h
+ChemCompt.o: VoxelJunction.h ChemCompt.h MeshEntry.h Boundary.h
+MeshCompt.o: VoxelJunction.h ChemCompt.h MeshCompt.h MeshEntry.h Boundary.h
+CylBase.o: ../utility/Vec.h CylBase.h
+CylMesh.o: ../utility/Vec.h VoxelJunction.h ChemCompt.h CylBase.h CylMesh.h MeshEntry.h Boundary.h
+CubeMesh.o: VoxelJunction.h ChemCompt.h CubeMesh.h MeshEntry.h Boundary.h
+NeuroNode.o: CylBase.h NeuroNode.h
+NeuroMesh.o: ../basecode/SparseMatrix.h ChemCompt.h CylBase.h NeuroNode.h NeuroMesh.h
+SpineMesh.o: ../basecode/SparseMatrix.h VoxelJunction.h ChemCompt.h CylBase.h NeuroNode.h NeuroMesh.h ../utility/Vec.h SpineEntry.h SpineMesh.h
+SpineEntry.o: VoxelJunction.h ChemCompt.h CylBase.h ../utility/Vec.h SpineEntry.h
+PsdMesh.o: ../basecode/SparseMatrix.h VoxelJunction.h ChemCompt.h CylBase.h ../utility/Vec.h SpineEntry.h SpineMesh.h
+testMesh.o: ../basecode/SparseMatrix.h CylBase.h NeuroNode.h MeshEntry.h ChemCompt.h CylMesh.h Boundary.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
+
diff --git a/moose-core/mpi/Makefile b/moose-core/mpi/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..a127fb78de6ffe176ee224b266771deb17c782a3
--- /dev/null
+++ b/moose-core/mpi/Makefile
@@ -0,0 +1,34 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2013 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _mpi.o
+
+OBJ = \
+ PostMaster.o \
+ testMpi.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+Postmaster.o: PostMaster.h
+testMpi.o: PostMaster.h
+
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/msg/Makefile b/moose-core/msg/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..1a373925f150d72886420d1b1fbd243d038334b0
--- /dev/null
+++ b/moose-core/msg/Makefile
@@ -0,0 +1,44 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _msg.o
+
+OBJ = \
+ Msg.o \
+ DiagonalMsg.o \
+ OneToAllMsg.o \
+ OneToOneMsg.o \
+ SingleMsg.o \
+ SparseMsg.o \
+ OneToOneDataIndexMsg.o \
+ testMsg.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+DiagonalMsg.o: DiagonalMsg.h
+OneToAll.o: OneToAll.h
+OneToOne.o: OneToOne.h
+OneToOneDataIndex.o: OneToOneDataIndex.h
+SingleMsg.o: SingleMsg.h
+SparseMsg.o: SparseMsg.h
+testMsg.o: DiagonalMsg.h OneToAllMsg.h OneToOneMsg.h SingleMsg.h SparseMsg.h OneToOneDataIndexMsg.h ../basecode/SetGet.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/msg/SparseMsg.cpp b/moose-core/msg/SparseMsg.cpp
index 65051f64d1e6f24b8c0cf60444bf9e75c937b62f..44f79d135eac65ea8109b40d370e3d816af26c8e 100644
--- a/moose-core/msg/SparseMsg.cpp
+++ b/moose-core/msg/SparseMsg.cpp
@@ -215,14 +215,11 @@ void SparseMsg::updateAfterFill()
{
unsigned int startData = e2_->localDataStart();
unsigned int endData = startData + e2_->numLocalData();
- SparseMatrix< unsigned int > temp( matrix_);
- temp.transpose();
- for ( unsigned int i = 0; i < temp.nRows(); ++ i ) {
+ for ( unsigned int i = 0; i < matrix_.nRows(); ++ i ) {
+ const unsigned int* colIndex;
+ const unsigned int* entry;
+ unsigned int num = matrix_.getRow( i, &entry, &colIndex );
if ( i >= startData && i < endData ) {
- const unsigned int* colIndex;
- const unsigned int* entry;
- // SparseMatrix::getRow returns # of entries.
- unsigned int num = temp.getRow( i, &entry, &colIndex );
e2_->resizeField( i - startData, num );
}
}
diff --git a/moose-core/pymoose/Makefile b/moose-core/pymoose/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..1c8abeca9e00a0b2bd0c0b36cf9fb222ebfbdd5d
--- /dev/null
+++ b/moose-core/pymoose/Makefile
@@ -0,0 +1,22 @@
+# Makefile
+#
+# Author: Subhasis Ray
+# Created: 2011-03-10 12:10:32 (+0530)
+TARGET = _pymoose.o
+# CXXFLAGS += -I../basecode -I../msg -I../shell
+CXXFLAGS += -DQUIET_MODE
+NUMPY_WARNING_FLAG = -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+.PHONY: clean
+
+HEADERS = moosemodule.h ../basecode/global.h PyRun.h
+
+OBJ = moosemodule.o mfield.o vec.o melement.o test_moosemodule.o PyRun.o
+
+$(TARGET): $(OBJ) $(HEADERS) ../basecode/main.cpp ../utility/_utility.o ../basecode/_basecode.o
+ $(LD) -r -o $(TARGET) $(OBJ) $(LDFLAGS)
+
+.cpp.o: $(HEADERS)
+ $(CXX) $(CXXFLAGS) $(NUMPY_WARNING_FLAG) -I.. -I../basecode $< -c
+clean:
+ -rm -f *.o
+
diff --git a/moose-core/pymoose/mfield.cpp b/moose-core/pymoose/mfield.cpp
index 7995427f2a9e40e0171c4af41e6936ce2ca02607..7e73f2650e979d17ef72952699f4274121f3358c 100644
--- a/moose-core/pymoose/mfield.cpp
+++ b/moose-core/pymoose/mfield.cpp
@@ -316,7 +316,7 @@ PyObject * moose_DestField_call(PyObject * self, PyObject * args,
PyObject * arg = PyTuple_GetItem(args, ii);
Py_INCREF(arg);
PyTuple_SetItem(newargs, ii+1, arg);
- // Py_DECREF(arg);
+ Py_DECREF(arg);
}
// Call ObjId._setDestField with the new arguments
PyObject * ret = moose_ObjId_setDestField(((_Field*)self)->owner, newargs);
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
index 7f3d8535843986d1d0620b02a63fa8e1487d95fb..5747765be0fa07ee7de5ca40547e1ad4b162590a 100644
--- a/moose-core/python/moose/SBML/readSBML.py
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -459,8 +459,6 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue):
for ritem in range(0, model.getNumReactions()):
reactionCreated = False
groupName = ""
- rName = ""
- rId = ""
reac = model.getReaction(ritem)
if (reac.isSetId()):
rId = reac.getId()
diff --git a/moose-core/python/moose/SBML/writeSBML.py b/moose-core/python/moose/SBML/writeSBML.py
index 3f39cc3bffa8d1e6941c05dcbf5c6aa814e1053c..7bf1727e3d0533fb0f69b6c1ef72fbdcdc4248c6 100644
--- a/moose-core/python/moose/SBML/writeSBML.py
+++ b/moose-core/python/moose/SBML/writeSBML.py
@@ -20,7 +20,8 @@ Last-Updated: Wed Jan 11 15:20:00 2017(+0530)
'''
import sys
import re
-#from collections import Counter
+from collections import Counter
+
import moose
from .validation import validateModel
from moose.chemUtil.chemConnectUtil import *
@@ -420,13 +421,11 @@ def parmUnit(rct_order, cremodel_):
return unit_stream
-def Counter(items):
- return dict((i, items.count(i)) for i in items)
-
def getSubprd(cremodel_, mobjEnz, type, neighborslist):
if type == "sub":
reacSub = neighborslist
reacSubCou = Counter(reacSub)
+
# print " reacSubCou ",reacSubCou,"()",len(reacSubCou)
noofSub = len(reacSubCou)
rate_law = " "
diff --git a/moose-core/python/moose/chemUtil/chemConnectUtil.py b/moose-core/python/moose/chemUtil/chemConnectUtil.py
index a89516833e5a3899552942174108174d6363d608..93d8be9d1442970c5ac748184f6743ba6810fc6b 100644
--- a/moose-core/python/moose/chemUtil/chemConnectUtil.py
+++ b/moose-core/python/moose/chemUtil/chemConnectUtil.py
@@ -1,6 +1,6 @@
import moose
import numpy as np
-#from collections import Counter
+from collections import Counter
def xyPosition(objInfo,xory):
try:
@@ -177,6 +177,5 @@ def countitems(mitems,objtype):
items = []
items = moose.element(mitems).neighbors[objtype]
uniqItems = set(items)
- #countuniqItems = Counter(items)
- countuniqItems = dict((i, items.count(i)) for i in items)
+ countuniqItems = Counter(items)
return(uniqItems,countuniqItems)
\ No newline at end of file
diff --git a/moose-core/python/moose/genesis/writeKkit.py b/moose-core/python/moose/genesis/writeKkit.py
index 11b14c951280e4ddf4e700ae14b07f961bca34fd..ba71603148d5e5096a41e14499027a7a11b442c2 100644
--- a/moose-core/python/moose/genesis/writeKkit.py
+++ b/moose-core/python/moose/genesis/writeKkit.py
@@ -41,86 +41,75 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
if filename.rfind('.') != -1:
filename = filename[:filename.rfind('.')]
else:
- error = " "
- ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
- matplotcolor = {}
- for name,hexno in matplotlib.colors.cnames.items():
- matplotcolor[name]=hexno
-
- if filename.rfind('.') != -1:
- filename = filename[:filename.rfind('.')]
- else:
- filename = filename[:len(filename)]
- filename = filename+'.g'
- global NA
- NA = 6.0221415e23
- global cmin,cmax,xmin,xmax,ymin,ymax
- cmin, xmin, ymin = 0, 0, 0
- cmax, xmax, ymax = 1, 1, 1
-
- compt = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]')
- maxVol = estimateDefaultVol(compt)
- positionInfoExist = True
- if compt:
- if bool(sceneitems):
- cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
- elif not bool(sceneitems):
- srcdesConnection = {}
- setupItem(modelpath,srcdesConnection)
- meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,sceneitems = setupMeshObj(modelpath)
- if not positionInfoExist:
- #cmin,cmax,sceneitems = autoCoordinates(meshEntry,srcdesConnection)
- sceneitems = autoCoordinates(meshEntry,srcdesConnection)
-
- if not positionInfoExist:
- # if position are not from kkit, then zoom factor is applied while
- # writing to genesis. Like if position is from pyqtSceneItem or auto-coordinates
- cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
- for k,v in list(sceneitems.items()):
- anno = moose.element(k.path+'/info')
- # x1 = calPrime(v['x'])
- # y1 = calPrime(v['y'])
- # sceneitems[k]['x'] = x1
- # sceneitems[k]['y'] = y1
-
- f = open(filename, 'w')
- writeHeader (f,maxVol)
-
- gtId_vol = writeCompartment(modelpath,compt,f)
- writePool(modelpath,f,gtId_vol,sceneitems)
- error = ""
- reacList = writeReac(modelpath,f,sceneitems)
- enzList = writeEnz(modelpath,f,sceneitems)
- error = writeSumtotal(modelpath,f,error)
- error = writeStimulus(modelpath,f,error)
- f.write("simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
- "simundump xgraph /graphs/conc2 0 0 100 0 1 0\n")
- tgraphs = moose.wildcardFind(modelpath+'/##[ISA=Table2]')
- first, second = " ", " "
- if tgraphs:
- first,second = writeplot(tgraphs,f)
- if first:
- f.write(first)
- f.write("simundump xgraph /moregraphs/conc3 0 0 100 0 1 0\n"
- "simundump xgraph /moregraphs/conc4 0 0 100 0 1 0\n")
- if second:
- f.write(second)
- f.write("simundump xcoredraw /edit/draw 0 -6 4 -2 6\n"
- "simundump xtree /edit/draw/tree 0 \\\n"
- " /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
- "simundump xtext /file/notes 0 1\n")
- storeReacMsg(reacList,f)
- storeEnzMsg(enzList,f)
- if tgraphs:
- storePlotMsgs(tgraphs,f)
- writeFooter1(f)
- writeNotes(modelpath,f)
- writeFooter2(f)
- print('Written to file '+filename)
- return error,True
- else:
- print(("Warning: writeKkit:: No model found on " , modelpath))
- return False
+ filename = filename[:len(filename)]
+ filename = filename+'.g'
+ global NA
+ NA = 6.0221415e23
+ global cmin,cmax,xmin,xmax,ymin,ymax
+ cmin, xmin, ymin = 0, 0, 0
+ cmax, xmax, ymax = 1, 1, 1
+
+ compt = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]')
+ maxVol = estimateDefaultVol(compt)
+ positionInfoExist = True
+ if compt:
+ if bool(sceneitems):
+ cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
+ elif not bool(sceneitems):
+ srcdesConnection = {}
+ setupItem(modelpath,srcdesConnection)
+ meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,sceneitems = setupMeshObj(modelpath)
+ if not positionInfoExist:
+ #cmin,cmax,sceneitems = autoCoordinates(meshEntry,srcdesConnection)
+ sceneitems = autoCoordinates(meshEntry,srcdesConnection)
+
+ if not positionInfoExist:
+ # if position are not from kkit, then zoom factor is applied while
+ # writing to genesis. Like if position is from pyqtSceneItem or auto-coordinates
+ cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
+ for k,v in list(sceneitems.items()):
+ anno = moose.element(k.path+'/info')
+ x1 = calPrime(v['x'])
+ y1 = calPrime(v['y'])
+ sceneitems[k]['x'] = x1
+ sceneitems[k]['y'] = y1
+
+ f = open(filename, 'w')
+ writeHeader (f,maxVol)
+
+ gtId_vol = writeCompartment(modelpath,compt,f)
+ writePool(modelpath,f,gtId_vol,sceneitems)
+ reacList = writeReac(modelpath,f,sceneitems)
+ enzList = writeEnz(modelpath,f,sceneitems)
+ writeSumtotal(modelpath,f)
+ f.write("simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
+ "simundump xgraph /graphs/conc2 0 0 100 0 1 0\n")
+ tgraphs = moose.wildcardFind(modelpath+'/##[ISA=Table2]')
+ first, second = " ", " "
+ if tgraphs:
+ first,second = writeplot(tgraphs,f)
+ if first:
+ f.write(first)
+ f.write("simundump xgraph /moregraphs/conc3 0 0 100 0 1 0\n"
+ "simundump xgraph /moregraphs/conc4 0 0 100 0 1 0\n")
+ if second:
+ f.write(second)
+ f.write("simundump xcoredraw /edit/draw 0 -6 4 -2 6\n"
+ "simundump xtree /edit/draw/tree 0 \\\n"
+ " /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
+ "simundump xtext /file/notes 0 1\n")
+ storeReacMsg(reacList,f)
+ storeEnzMsg(enzList,f)
+ if tgraphs:
+ storePlotMsgs(tgraphs,f)
+ writeFooter1(f)
+ writeNotes(modelpath,f)
+ writeFooter2(f)
+ print('Written to file '+filename)
+ return True
+ else:
+ print(("Warning: writeKkit:: No model found on " , modelpath))
+ return False
def findMinMax(sceneitems):
cmin = 0.0
@@ -333,45 +322,15 @@ def trimPath(mobj):
s = splitpath.replace("_dash_",'-')
return s
-def writeSumtotal( modelpath,f, error):
+def writeSumtotal( modelpath,f):
funclist = moose.wildcardFind(modelpath+'/##[ISA=Function]')
- s = ""
for func in funclist:
- fInfound = True
- fOutfound = True
funcInputs = moose.element(func.path+'/x[0]')
- if not len(funcInputs.neighbors["input"]):
- fInfound = False
- error = error +'\n/'+ (moose.element(func)).parent.name+ '/'+moose.element(func).name + ' function doesn\'t have input which is not allowed in genesis. \n This function is not written down into genesis file\n'
-
- if not len(func.neighbors["valueOut"]):
- error = error +'Function'+func.path+' has not been connected to any output, this function is not written to genesis file'
- fOutfound = False
- else:
- for srcfunc in func.neighbors["valueOut"]:
- if srcfunc.className in ["ZombiePool","ZombieBufPool","Pool","BufPool"]:
- functionOut = moose.element(srcfunc)
- else:
- error = error +'Function output connected to '+srcfunc.name+ ' which is a '+ srcfunc.className+' which is not allowed in genesis, this function '+(moose.element(func)).path+' is not written to file'
- fOutfound = False
-
- if fInfound and fOutfound:
- srcPool = []
- for funcInput in funcInputs.neighbors["input"]:
- if funcInput not in srcPool:
- srcPool.append(funcInput)
- s = "addmsg /kinetics/" + trimPath(funcInput)+ " /kinetics/"+ trimPath(functionOut)+ " SUMTOTAL n nInit\n"
- f.write(s)
- else:
- error = error + '\n Genesis doesn\'t allow same moluecule connect to function mutiple times. \n Pool \''+ moose.element(funcInput).name + '\' connected to '+ (moose.element(func)).path
- return error
-
-def writeStimulus(modelpath,f,error):
-
- if len(moose.wildcardFind(modelpath+'/##[ISA=StimulusTable]')):
- error = error +'\n StimulusTable is not written into genesis. This is in Todo List'
+ s = ""
+ for funcInput in funcInputs.neighbors["input"]:
+ s = s+ "addmsg /kinetics/" + trimPath(funcInput)+ " /kinetics/" + trimPath(moose.element(func.parent)) + " SUMTOTAL n nInit\n"
+ f.write(s)
- return error
def storePlotMsgs( tgraphs,f):
s = ""
if tgraphs:
diff --git a/moose-core/python/moose/merge/merge.py b/moose-core/python/moose/merge/merge.py
index 224431d431935a0592064b731ecdc685aa648dff..f76ca494b3daffccc1fa6318dd9783564c3a09d1 100644
--- a/moose-core/python/moose/merge/merge.py
+++ b/moose-core/python/moose/merge/merge.py
@@ -30,40 +30,9 @@ import mtypes
from moose.chemUtil.chemConnectUtil import *
from moose.chemUtil.graphUtils import *
-from moose.genesis import mooseWriteKkit
def mergeChemModel(A,B):
""" Merges two model or the path """
- A = src
- B = des
- loadedA = False
- loadedB = False
- modelA = moose.element('/')
- modelB = moose.element('/')
-
- if os.path.isfile(A):
- modelA,loadedA = loadModels(A)
-
- elif moose.exists(A):
- modelA = A
- loadedA = True
- else:
- print ("%s path or file doesnot exists. Mergering will exist" % (A))
- exit(0)
-
- if os.path.isfile(B):
- modelB,loadedB = loadModels(B)
- elif moose.exists(B):
- modelB = B
- loadedB = True
- else:
- print ("%s path or file doesnot exists. Mergering will exist " % (B))
- exit(0)
-
- if loadedA and loadedB:
- ## yet deleteSolver is called to make sure all the moose object are off from solver
- deleteSolver(modelA)
- deleteSolver(modelB)
modelA,loadedA = loadModels(A)
modelB,loadedB = loadModels(B)
@@ -115,19 +84,14 @@ def mergeChemModel(A,B):
funcNotallowed = []
funcNotallowed = functionMerge(dictComptA,dictComptB,key)
- poolListinb = updatePoolList(dictComptB)
- R_Duplicated,R_Notcopiedyet,R_Daggling = reacMerge(dictComptB,dictComptA,key,poolListinb)
-
- poolListinb = updatePoolList(dictComptB)
- E_Duplicated,E_Notcopiedyet,E_Daggling = enzymeMerge(dictComptB,dictComptA,key,poolListinb)
- spath, sfile = os.path.split(src)
- dpath, dfile = os.path.split(des)
- print("\nThe content of %s (src) model is merged to %s (des)." %(sfile, dfile))
- # Here any error or warning during Merge is written it down
- if funcExist:
- print( "\nIn model \"%s\" pool already has connection from a function, these function from model \"%s\" is not allowed to connect to same pool,\n since no two function are allowed to connect to same pool:"%(dfile, sfile))
- for fl in list(funcExist):
- print("\t [Pool]: %s [Function]: %s \n" %(str(fl.parent.name), str(fl.path)))
+ poolListina = updatePoolList(dictComptA)
+ R_Duplicated,R_Notcopiedyet,R_Daggling = reacMerge(dictComptA,dictComptB,key,poolListina)
+
+ poolListina = updatePoolList(dictComptA)
+ E_Duplicated,E_Notcopiedyet,E_Daggling = enzymeMerge(dictComptA,dictComptB,key,poolListina)
+
+ print("\n Model is merged to %s" %modelA)
+
if funcNotallowed:
print( "\nPool already connected to a function, this function is not to connect to same pool, since no two function are allowed to connect to same pool:")
for fl in list(funcNotallowed):
@@ -169,34 +133,8 @@ def mergeChemModel(A,B):
if E_Daggling:
print ("Enzyme:")
for ed in list(E_Daggling):
- print ("%s " %str(ed.name))
- ## Model is saved
- print ("\n ")
- savemodel = raw_input("Do you want to save the model? \"YES\" \"NO\" ")
- if savemodel.lower() == 'yes' or savemodel.lower() == 'y':
- mergeto = raw_input("Enter File name ")
- if mergeto and mergeto.strip():
- filenameto = 'merge.g'
- else:
- if str(mergeto).rfind('.') != -1:
- mergeto = mergeto[:str(mergeto).rfind('.')]
- if str(mergeto).rfind('/'):
- mergeto = mergeto+'merge'
-
- filenameto = mergeto+'.g'
-
- error,written = moose.mooseWriteKkit(modelB, filenameto)
- if written == False:
- print('Could not save the Model, check the files')
- else:
- if error == "":
- print(" \n The merged model is saved into \'%s\' " %(filenameto))
- else:
- print('Model is saved but these are not written\n %s' %(error))
- else:
- print ('\nMerged model is available under moose.element(\'%s\')' %(modelB))
- print (' If you are in python terminal you could save \n >moose.mooseWriteKkit(\'%s\',\'filename.g\')' %(modelB))
-
+ print ("%s " %str(ed.name))
+
def functionMerge(comptA,comptB,key):
funcNotallowed = []
comptApath = moose.element(comptA[key]).path
@@ -295,9 +233,7 @@ def loadModels(filename):
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
- if moose.exists(modelpath):
- moose.delete(modelpath)
- moose.loadModel(filepath,modelpath)
+ moose.loadModel(filename,modelpath)
loaded = True
elif subtype == 'sbml':
@@ -667,40 +603,7 @@ def mooseIsInstance(element, classNames):
if __name__ == "__main__":
- try:
- sys.argv[1]
- except IndexError:
- print("Source filename or path not given")
- exit(0)
- else:
- src = sys.argv[1]
- if not os.path.exists(src):
- print("Filename or path does not exist",src)
- else:
- try:
- sys.argv[2]
- except IndexError:
- print("Destination filename or path not given")
- exit(0)
- else:
- des = sys.argv[2]
- if not os.path.exists(src):
- print("Filename or path does not exist",des)
- exit(0)
- else:
- mergered = mergeChemModel(src,des)
- '''
- try:
- sys.argv[3]
- except IndexError:
- print ("Merge to save not specified")
- mergeto = "merge"
- else:
- mergeto = sys.argv[3]
- if str(mergeto).rfind('.') != -1:
- mergeto = mergeto[:str(mergeto).rfind('.')]
- if str(mergeto).rfind('/'):
- mergeto = mergeto+'merge'
-
- mergered = mergeChemModel(src,des,mergeto)
- '''
+
+ modelA = '/home/harsha/genesis_files/gfile/acc92.g'
+ modelB = '/home/harsha/genesis_files/gfile/acc50.g'
+ mergered = mergeChemModel(modelA,modelB)
diff --git a/moose-core/python/moose/plot_utils.py b/moose-core/python/moose/plot_utils.py
index c7c7a977acb07952362c14430e6857e1b2487802..b2740954dc10103f0c6e6f266ce08cb4cedeb315 100644
--- a/moose-core/python/moose/plot_utils.py
+++ b/moose-core/python/moose/plot_utils.py
@@ -300,13 +300,7 @@ def plot_records(data_dict, xvec = None, **kwargs):
subplot = kwargs.get('subplot', False)
filters = [ x.lower() for x in kwargs.get('filter', [])]
- ax = kwargs.get( 'ax', None )
- if ax is None:
- plt.figure(figsize=(10, 1.5*len(data_dict)))
- if not subplot:
- ax = plt.subplot( 1, 1, 1 )
- kwargs[ 'ax' ] = ax
-
+ plt.figure(figsize=(10, 1.5*len(data_dict)))
for i, k in enumerate(data_dict):
pu.info("+ Plotting for %s" % k)
plotThis = False
@@ -321,9 +315,8 @@ def plot_records(data_dict, xvec = None, **kwargs):
yvec = data_dict[k]
plotVector(yvec, xvec, label=k, **kwargs)
else:
- ax = plt.subplot(len(data_dict), 1, i+1)
- kwargs[ 'ax' ] = ax
- yvec = data_dict[k].vector
+ plt.subplot(len(data_dict), 1, i)
+ yvec = data_dict[k]
plotVector(yvec, xvec, label=k, **kwargs)
if subplot:
try:
diff --git a/moose-core/python/rdesigneur/rmoogli.py b/moose-core/python/rdesigneur/rmoogli.py
index 8a475a09a85544dcb3f82890747da8e64ab916b0..7f8fa883b372bea23ec50fc754653e93c3f5995c 100644
--- a/moose-core/python/rdesigneur/rmoogli.py
+++ b/moose-core/python/rdesigneur/rmoogli.py
@@ -65,9 +65,7 @@ def interlude( view ):
view.mooGroup.set("color", val, view.mapper)
view.yaw( rotation )
#print moogliDt, len( val ), runtime
- currt = moose.element("/clock").currentTime
- view.timecb.set_title( 'T = {:.3f} s'.format( currt ) )
- if currt >= runtime:
+ if moose.element("/clock").currentTime >= runtime:
view.stop()
# This func is used for later viewers, that don't handle advancing time.
@@ -148,34 +146,13 @@ def makeMoogli( rd, mooObj, moogliEntry, fieldInfo ):
moogliEntry[5],
moogliEntry[6]))
cb.set_num_labels(3)
-
- # Use the text title on a colorbar to display the current time!!
- # Spectacularly ugly hack, but I was unable to find other ways to put
- # text in a predefined place in a moogli view.
- timecb = moogli.widgets.ColorBar( id="timecb",
- title = "T = 0 s",
- text_color=moogli.colors.BLACK,
- position=moogli.geometry.Vec3f(0.1, -0.01, 0.0),
- size=moogli.geometry.Vec3f(0.01, 0.02, 0.0),
- text_font="/usr/share/fonts/truetype/ubuntu-font-family/Ubuntu-R.ttf",
- orientation=0.0,
- text_character_size=16,
- label_formatting_precision=1,
- colormap=moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow),
- color_resolution=2,
- scalar_range=moogli.geometry.Vec2f( 0.0, 1.0 )
- )
- timecb.set_num_labels( 0 )
-
view.attach_color_bar(cb)
- view.attach_color_bar(timecb)
view.rd = rd
view.mooObj = displayObj
view.mooGroup = updateGroup
view.mooField = mooField
view.mooScale = fieldInfo[2]
view.mapper = mapper
- view.timecb = timecb
viewer.attach_view(view)
return viewer
diff --git a/moose-core/randnum/Makefile b/moose-core/randnum/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..259bbb4c7882c99a7c45a5970251d0a9f49ac921
--- /dev/null
+++ b/moose-core/randnum/Makefile
@@ -0,0 +1,51 @@
+CXXFLAGS += -I..
+# the line below are for easy inclusion of libxml++
+#CXXFLAGS += $(shell pkg-config libxml++-2.6 --CXXFLAGS)
+
+TARGET = _randnum.o
+
+OBJ = \
+ mt19937ar.o \
+ RandGenerator.o \
+ UniformRng.o \
+ Uniform.o \
+ Exponential.o \
+ ExponentialRng.o \
+ Binomial.o \
+ Normal.o \
+ Poisson.o \
+ Gamma.o \
+ PoissonRng.o \
+ NormalRng.o \
+ BinomialRng.o \
+ GammaRng.o \
+
+HEADERS = \
+ ../basecode/header.h \
+ randnum.h \
+ Probability.h \
+ RandGenerator.h \
+ UniformRng.h \
+ Uniform.h \
+ Exponential.h \
+ ExponentialRng.h \
+ Binomial.h \
+ Gamma.h \
+ Poisson.h \
+ PoissonRng.h \
+ Normal.h \
+ NormalRng.h \
+ BinomialRng.h \
+ GammaRng.h \
+
+default: $(TARGET)
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $< -c
+# $(CXX) $(CXXFLAGS) $(shell pkg-config libxml++-2.6 --CXXFLAGS) $< -c
+
+$(TARGET): $(OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/scheduling/Makefile b/moose-core/scheduling/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..2061a090a4a12a018e047a11c1db4c2416c0b4e9
--- /dev/null
+++ b/moose-core/scheduling/Makefile
@@ -0,0 +1,34 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2009 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _scheduling.o
+
+OBJ = \
+ Clock.o \
+ testScheduling.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+Clock.o: Clock.h
+testScheduling.o: Clock.h
+
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/shell/Makefile b/moose-core/shell/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..543301438d3e165da180a7ee2109b498a1bd4023
--- /dev/null
+++ b/moose-core/shell/Makefile
@@ -0,0 +1,49 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _shell.o
+
+OBJ = \
+ Shell.o \
+ ShellCopy.o \
+ ShellThreads.o \
+ LoadModels.o \
+ SaveModels.o \
+ Neutral.o \
+ Wildcard.o \
+ testShell.o \
+
+HEADERS = \
+ ../basecode/header.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+#Shell.o: Shell.h Neutral.h ../scheduling/Clock.h ../sbml/MooseSbmlWriter.h ../sbml/MooseSbmlReader.h
+Shell.o: Shell.h Neutral.h ../scheduling/Clock.h
+ShellCopy.o: Shell.h Neutral.h ../scheduling/Clock.h
+ShellSetGet.o: Shell.h
+ShellThreads.o: Shell.h Neutral.h ../scheduling/Clock.h
+LoadModels.o: Shell.h Neutral.h ../biophysics/SwcSegment.h ../biophysics/ReadSwc.h
+SaveModels.o: Shell.h Neutral.h
+Neutral.o: Neutral.h ../basecode/ElementValueFinfo.h
+Wildcard.o: Wildcard.h Shell.h Neutral.h ../basecode/ElementValueFinfo.h
+testShell.o: Wildcard.h Shell.h Neutral.h ../builtins/Arith.h ../basecode/SparseMatrix.h ../msg/SparseMsg.h ../msg/SingleMsg.h ../basecode/SetGet.h ../basecode/HopFunc.h ../basecode/OpFuncBase.h ../basecode/OpFunc.h
+
+#../kinetics/ReadKkit.h ../biophysics/ReadCell.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../basecode -I../msg $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
+
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/signeur/Makefile b/moose-core/signeur/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..ad8c507467241ca0853937796d8b21b8e10b9b8f
--- /dev/null
+++ b/moose-core/signeur/Makefile
@@ -0,0 +1,36 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** Copyright (C) 2003-2012 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+CXXFLAGS += -I..
+# the line below are for easy inclusion of libxml++
+#CXXFLAGS += $(shell pkg-config libxml++-2.6 --cflags)
+
+TARGET = _signeur.o
+
+OBJ = \
+ Adaptor.o \
+ testSigNeur.o
+
+
+HEADERS = \
+ ../basecode/header.h \
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+Adaptor.o: Adaptor.h
+testSigNeur.o: Adaptor.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) -I.. -I../basecode $< -c
+
+$(TARGET): $(OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ)
+clean:
+ -rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/synapse/Makefile b/moose-core/synapse/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..bbf82b990c89bb574aab8b2fd4ff27857a97a6d1
--- /dev/null
+++ b/moose-core/synapse/Makefile
@@ -0,0 +1,50 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+TARGET = _synapse.o
+
+OBJ = \
+ SynHandlerBase.o \
+ SimpleSynHandler.o \
+ STDPSynHandler.o \
+ GraupnerBrunel2012CaPlasticitySynHandler.o \
+ Synapse.o \
+ STDPSynapse.o \
+ RollingMatrix.o \
+ SeqSynHandler.o \
+ testSynapse.o \
+
+# GSL_LIBS = -L/usr/lib -lgsl
+
+HEADERS = \
+ ../basecode/header.h \
+ ../utility/numutil.h \
+
+
+default: $(TARGET)
+
+$(OBJ) : $(HEADERS)
+SynHandlerBase.o: SynHandlerBase.h Synapse.h
+SimpleSynHandler.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SynEvent.h
+STDPSynHandler.o: SynHandlerBase.h STDPSynapse.h STDPSynHandler.h SynEvent.h
+GraupnerBrunel2012CaPlasticitySynHandler.o: SynHandlerBase.h Synapse.h GraupnerBrunel2012CaPlasticitySynHandler.h SynEvent.h
+Synapse.o: Synapse.h SynHandlerBase.h
+STDPSynapse.o: STDPSynapse.h SynHandlerBase.h
+RollingMatrix.o: RollingMatrix.h
+SeqSynHandler.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SeqSynHandler.h RollingMatrix.h SynEvent.h
+testSynapse.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SeqSynHandler.h RollingMatrix.h SynEvent.h
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg -I .. -I../external/muparser/include $< -c
+
+$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
+
+clean:
+ rm -f *.o $(TARGET) core core.*
diff --git a/moose-core/synapse/SeqSynHandler.cpp b/moose-core/synapse/SeqSynHandler.cpp
index 7cdf6bc98d02fb54903294d77509018201d79ff6..51a231ed50906b42e5efcf78e349102244abd57b 100644
--- a/moose-core/synapse/SeqSynHandler.cpp
+++ b/moose-core/synapse/SeqSynHandler.cpp
@@ -105,19 +105,6 @@ const Cinfo* SeqSynHandler::initCinfo()
&SeqSynHandler::setWeightScale,
&SeqSynHandler::getWeightScale
);
-
- static ValueFinfo< SeqSynHandler, double > sequencePower(
- "sequencePower",
- "Exponent for the outcome of the sequential calculations. "
- "This is needed because linear summation of terms in the kernel"
- "means that a brief stong sequence match is no better than lots"
- "of successive low matches. In other words, 12345 is no better"
- "than 11111. Using an exponent lets us select the former."
- "Defaults to 1.0.",
- &SeqSynHandler::setSequencePower,
- &SeqSynHandler::getSequencePower
- );
-
static ReadOnlyValueFinfo< SeqSynHandler, vector< double > >
weightScaleVec(
"weightScaleVec",
@@ -141,14 +128,10 @@ const Cinfo* SeqSynHandler::initCinfo()
&kernelWidth, // Field
&seqDt, // Field
&historyTime, // Field
- &sequenceScale, // Field
- &baseScale, // Field
- &synapseOrder, // Field
- &synapseOrderOption, // Field
- &seqActivation, // ReadOnlyField
- &plasticityScale, // Field
- &sequencePower, // Field
- &weightScaleVec, // ReadOnlyField
+ &responseScale, // Field
+ &seqActivation, // Field
+ &weightScale, // Field
+ &weightScaleVec, // Field
&kernel, // ReadOnlyField
&history // ReadOnlyField
};
@@ -177,12 +160,9 @@ SeqSynHandler::SeqSynHandler()
kernelWidth_( 5 ),
historyTime_( 2.0 ),
seqDt_ ( 1.0 ),
- baseScale_( 0.0 ),
- sequenceScale_( 1.0 ),
- plasticityScale_( 0.0 ),
- sequencePower_( 1.0 ),
- seqActivation_( 0.0 ),
- synapseOrderOption_( -1 ) // sequential ordering
+ responseScale_( 1.0 ),
+ weightScale_( 0.0 ),
+ seqActivation_( 0.0 )
{
int numHistory = static_cast< int >( 1.0 + floor( historyTime_ * (1.0 - 1e-6 ) / seqDt_ ) );
history_.resize( numHistory, 0 );
@@ -335,17 +315,7 @@ vector< double >SeqSynHandler::getWeightScaleVec() const
return weightScaleVec_;
}
-double SeqSynHandler::getSequencePower() const
-{
- return sequencePower_;
-}
-
-void SeqSynHandler::setSequencePower( double v )
-{
- sequencePower_ = v;
-}
-
-vector< double >SeqSynHandler::getWeightScaleVec() const
+void SeqSynHandler::setWeightScale( double v )
{
weightScale_ = v;
}
@@ -424,7 +394,7 @@ void SeqSynHandler::vProcess( const Eref& e, ProcPtr p )
seqActivation_ = 0.0;
for ( vector< double >::iterator y = correlVec.begin();
y != correlVec.end(); ++y )
- seqActivation_ += pow( *y, sequencePower_ );
+ seqActivation_ += *y;
// We'll use the seqActivation_ to send a special msg.
seqActivation_ *= responseScale_;
diff --git a/moose-core/synapse/SeqSynHandler.h b/moose-core/synapse/SeqSynHandler.h
index 15e1472f5248c8c83876c5dd144faf65eff47172..55fd01181bcf868b610c0192456fc04f5c05b71d 100644
--- a/moose-core/synapse/SeqSynHandler.h
+++ b/moose-core/synapse/SeqSynHandler.h
@@ -58,10 +58,8 @@ class SeqSynHandler: public SynHandlerBase
void setResponseScale( double v );
double getResponseScale() const;
double getSeqActivation() const; // summed activation of syn chan
- void setPlasticityScale( double v );
- double getPlasticityScale() const;
- void setSequencePower( double v );
- double getSequencePower() const;
+ void setWeightScale( double v );
+ double getWeightScale() const;
vector< double > getWeightScaleVec() const;
vector< double > getKernel() const;
vector< double > getHistory() const;
@@ -94,15 +92,6 @@ class SeqSynHandler: public SynHandlerBase
// Scaling factor for weight changes in each synapse from response
double weightScale_;
- /**
- * Exponent to use for the outcome of the sequential calculations.
- * This is needed because linear summation of terms in the kernel
- * means that a brief stong sequence match is no better than lots
- * of successive low matches. In other words, 12345 is no better
- * than 11111.
- */
- double sequencePower_;
-
///////////////////////////////////////////
// Some readonly fields
double seqActivation_; // global activation if sequence recognized
diff --git a/moose-core/utility/Makefile b/moose-core/utility/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..87af0b7dc6bf3ae2edd3e7517cc15831d4e4679c
--- /dev/null
+++ b/moose-core/utility/Makefile
@@ -0,0 +1,45 @@
+#/**********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment.
+#** Copyright (C) 2003-2012 Upinder S. Bhalla. and NCBS
+#** It is made available under the terms of the
+#** GNU Lesser General Public License version 2.1
+#** See the file COPYING.LIB for the full notice.
+#**********************************************************************/
+
+CXXFLAGS += -I..
+# the line below are for easy inclusion of libxml++
+#CXXFLAGS += $(shell pkg-config libxml++-2.6 --cflags)
+
+TARGET = _utility.o
+
+OBJ = \
+ strutil.o \
+ types.o \
+ setupenv.o \
+ numutil.o \
+ Annotator.o \
+ cnpy.o \
+ Vec.o \
+
+
+HEADERS = \
+ strutil.h \
+ numutil.h \
+ ../basecode/header.h \
+ cnpy.hpp \
+
+default: $(TARGET)
+
+strutil.o: strutil.h
+Annotator.o: Annotator.h
+Vec.o: Vec.h ../basecode/doubleEq.h
+cnpy.o : cnpy.hpp
+
+.cpp.o:
+ $(CXX) $(CXXFLAGS) -I.. -I../basecode $< -c
+
+$(TARGET): $(OBJ) $(HEADERS)
+ $(LD) -r -o $(TARGET) $(OBJ)
+clean:
+ -rm -f *.o $(TARGET) core core.*