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Make all_modules and all_clean compiles in parallel. Added NEEDED_MODULES

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This commit is contained in:
Anthony Scemama 2014-04-03 11:19:41 +02:00
parent c5ac0c5970
commit f9f3fac7ff
30 changed files with 272 additions and 124 deletions
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1
README.rst
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@ -1,3 +1,4 @@
===============
Quantum package
===============

4
scripts/check_dependencies.sh
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@ -25,7 +25,7 @@ fi
if [[ $1 == "-" ]]
then
COMMAND_LINE=$(grep -e "^INCLUDE_DIRS" Makefile 2>/dev/null | cut -d '=' -f 2)
COMMAND_LINE=$(cat NEEDED_MODULES)
else
COMMAND_LINE=$(unique_list $@)
fi
@ -44,7 +44,7 @@ DEPS_LONG=""
for i in $COMMAND_LINE
do
DEPS_LONG+=" $i "
DEPS_LONG+=$(grep -e '^INCLUDE_DIRS' ${QPACKAGE_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
DEPS_LONG+=$(cat ${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES)
done
DEPS=$(unique_list $DEPS_LONG)

12
scripts/create_Makefile.sh
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@ -11,7 +11,7 @@ DEPS_LONG=""
for i in $@
do
DEPS_LONG+=" $i "
DEPS_LONG+=$(grep 'INCLUDE_DIRS' ${QPACKAGE_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
DEPS_LONG+=$(cat ${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES)
done
DEPS=($(
@ -21,12 +21,16 @@ do
done | sort | uniq
))
# Create the NEEDED_MODULES file
cat << EOF > NEEDED_MODULES
${DEPS[@]}
EOF
# Create the Makefile
cat << EOF > Makefile
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS = ${DEPS[@]}
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -38,7 +42,7 @@ include \$(QPACKAGE_ROOT)/src/Makefile.config
include \$(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: \$(filter-out IRPF90_temp/%, \$(wildcard */*.irp.f)) \$(wildcard *.irp.f) \$(wildcard *.inc.f) Makefile \$(EZFIO)
irpf90.make: \$(filter-out IRPF90_temp/%, \$(wildcard */*.irp.f)) \$(wildcard *.irp.f) \$(wildcard *.inc.f) Makefile \$(EZFIO) NEEDED_MODULES
\$(IRPF90)
Makefile.depend: Makefile

2
scripts/create_Makefile_depend.sh
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@ -8,7 +8,7 @@
SRC=""
OBJ=""
DEPS=$(grep "INCLUDE_DIRS" Makefile 2>/dev/null | cut -d '=' -f 2)
DEPS=$(cat NEEDED_MODULES)
for M in ${DEPS}
do

75
scripts/create_module.sh
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@ -7,10 +7,35 @@
# All remaining aruments are dependencies.
# Thu Apr 3 01:44:58 CEST 2014
DEBUG=0
# If DEBUG=1, the print debug info.
function debug()
{
if [[ $DEBUG -eq 1 ]]
then
function debug()
{
echo "$@"
}
else
function debug()
{
}
fi
debug $@
}
MODULE=$1
shift
DEPS=$@
# Check if module already exists
if [ -d ${MODULE} ]
then
@ -18,11 +43,57 @@ then
exit 1
fi
debug "Module does not already exist: OK"
# Set up dependencies
ALL_MODULES=$(cat NEEDED_MODULES)
if [[ 1 -eq 0 ]] ; then # TODO
# Create module directory and go into it
mkdir ${MODULE}
cd ${MODULE}
if [[ ! mkdir ${QPACKAGE_ROOT}/src/${MODULE} ]]
then
print "Unable to create module directory."
exit 1
fi
if [[ ! -d ${QPACKAGE_ROOT}/src/${MODULE} ]]
then
print "Something strange happened: the"
print ${QPACKAGE_ROOT}/src/${MODULE}
print "directory was not created."
exit 1
fi
cd ${QPACKAGE_ROOT}/src/${MODULE}
if [[ ${PWD} != ${QPACKAGE_ROOT}/src/${MODULE} ]]
then
print "Something strange happened: we should be in"
print ${QPACKAGE_ROOT}/src/${MODULE}
print "but we are in"
print ${PWD}
exit 1
fi
debug "Module directory is created."
fi # TODO
# Create the Makefile
${QPACKAGE_ROOT}/create_Makefile.sh
# Update module list in main NEEDED_MODULES
ALL_MODULES+=" ${MODULE}"
cd ${QPACKAGE_ROOT}/src
echo ${ALL_MODULES} > NEEDED_MODULES
debug "Updated NEEDED_MODULES"

2
src/.gitignore vendored
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@ -6,4 +6,4 @@ Makefile.config
*tags
*.o
*.mod
*/Makefile.depend
*Makefile.depend

4
src/AOs/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS = Ezfio_files Nuclei Utils
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

1
src/AOs/NEEDED_MODULES Normal file
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@ -0,0 +1 @@
Ezfio_files Nuclei Utils

4
src/Bitmask/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS = AOs Electrons Ezfio_files MOs Nuclei Utils
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

1
src/Bitmask/NEEDED_MODULES Normal file
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@ -0,0 +1 @@
AOs Electrons Ezfio_files MOs Nuclei Utils

4
src/Electrons/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS = Ezfio_files
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

1
src/Electrons/NEEDED_MODULES Normal file
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@ -0,0 +1 @@
Ezfio_files

3
src/Electrons/README.rst Normal file
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@ -0,0 +1,3 @@
This module contains the data relative to electrons: the number of alpha and beta electrons.

4
src/Ezfio_files/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS =
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

0
src/Ezfio_files/NEEDED_MODULES Normal file
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15
src/Ezfio_files/get_unit_and_open.irp.f
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@ -1,5 +1,20 @@
integer function getUnitAndOpen(f,mode)
implicit none
BEGIN_DOC
! :f:
! file name
!
! :mode:
! 'R' : READ, UNFORMATTED
! 'W' : WRITE, UNFORMATTED
! 'r' : READ, FORMATTED
! 'w' : WRITE, FORMATTED
! 'a' : APPEND, FORMATTED
! 'x' : READ/WRITE, FORMATTED
!
END_DOC
character*(*) :: f
character*(128) :: new_f
integer :: iunit

4
src/MOs/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS = AOs Ezfio_files Nuclei Utils
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

1
src/MOs/NEEDED_MODULES Normal file
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@ -0,0 +1 @@
AOs Ezfio_files Nuclei Utils

12
src/MOs/README.rst Normal file
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@ -0,0 +1,12 @@
Modifying MOs
=============
When modifying MOs, the label of the current MOs should change accordingly by changing the mo_label. For example:
.. code-block:: fortran
mo_coef = new_mo_coef
mo_label = "MyNewLabel"
TOUCH mo_coef mo_label

36
src/Makefile
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@ -1,23 +1,29 @@
default: all
INCLUDE_DIRS = Ezfio_files Nuclei Utils AOs Electrons MonoInts BiInts MOs Output Bitmask
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
include Makefile.common
include Makefile.config
LIB+=$(MKL)
SRC=BiInts/map_module.f90 Bitmask/bitmasks_module.f90
OBJ=IRPF90_temp/BiInts/map_module.o IRPF90_temp/Bitmask/bitmasks_module.o
PYTHON_SCRIPTS=
SRC=
OBJ=
include Makefile.depend
include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
all:$(ALL) $(PYTHON_SCRIPTS)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
all:$(ALL)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
all_clean:
for i in */ ; do unset INCLUDE_DIRS ; $(MAKE) -C $$i veryclean && $(MAKE) -C $$i clean_links ; done
Makefile.depend: Makefile NEEDED_MODULES
$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh
all_clean:
@for i in $(NEEDED_MODULES) ; do cd $$i ; make veryclean ; make clean_links ; cd .. ; done
all_modules: $(NEEDED_MODULES)
FORCE:
$(NEEDED_MODULES): FORCE
@cd $@ ; unset NEEDED_MODULES INCLUDE_DIRS ; make
all_modules:
for i in */ ; do unset INCLUDE_DIRS ; $(MAKE) -C $$i || exit 1 ; done

12
src/Makefile.common
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@ -2,11 +2,11 @@ ifndef QPACKAGE_ROOT
$(error QPACKAGE_ROOT undefined. Run the setup_environment.sh script)
endif
INCLUDE_DIRS_OK=$(shell X=`$(QPACKAGE_ROOT)/scripts/check_dependencies.sh $(INCLUDE_DIRS)` && echo OK || echo $$X)
ifneq ($(INCLUDE_DIRS_OK),OK)
NEEDED_MODULES_OK=$(shell X=`$(QPACKAGE_ROOT)/scripts/check_dependencies.sh $(NEEDED_MODULES)` && echo OK || echo $$X)
ifneq ($(NEEDED_MODULES_OK),OK)
$(info ---------------------)
$(info Your INCLUDE_DIRS variable is inconsistent. It should be:)
$(info INCLUDE_DIRS = $(INCLUDE_DIRS_OK))
$(info Your NEEDED_MODULES file is inconsistent. It should be:)
$(info $(NEEDED_MODULES))
$(info ---------------------)
$(error )
endif
@ -31,13 +31,13 @@ $(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_
@cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config
@cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
INCLUDE_DIRS+=include
INCLUDE_DIRS=$(NEEDED_MODULES) include
ifneq ($(PWD),$(QPACKAGE_ROOT)/src)
$(shell $(QPACKAGE_ROOT)/scripts/prepare_module.sh $(INCLUDE_DIRS))
clean_links:
rm $(INCLUDE_DIRS) $$(basename $$PWD)
rm -f $(INCLUDE_DIRS) $$(basename $$PWD)
else
clean_links:
endif

1
src/NEEDED_MODULES Normal file
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@ -0,0 +1 @@
AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils

4
src/Nuclei/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS = Ezfio_files Utils
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

1
src/Nuclei/NEEDED_MODULES Normal file
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@ -0,0 +1 @@
Ezfio_files Utils

4
src/Output/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS =
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

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@ -0,0 +1 @@

105
src/README.rst Normal file
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@ -0,0 +1,105 @@
======================
Programming guidelines
======================
Each module (directory) contains the following:
* A ``README.rst`` file to document the current module.
* An ``ASSUMPTIONS.rst`` file. This file should document all the implicit
assumptions used in the module. For example, if the atomic orbitals are
assumed to be normalized, this should be mentioned in the
``AOs/ASSUMPTIONS.rst`` file.
* A ``NEEDED_MODULES`` file which contains the list of modules on which the
current module depends
* A set of ``.irp.f`` files containing provider, subroutines and functions
* A ``tests`` directory that should contain the test programs of the module
(see testing section)
* A ``Makefile`` that should compile
* Optionally some ``*.ezfio_config`` configuration files for the EZFIO
library
A new module may be created by invoking the ``create_module.sh`` script.
Every subroutine, function or provider should be documented using the
BEGIN_DOC ... END_DOC block. The documentation should be written in
ReStructured Text format to enable the automatic generation of the Sphinx
documentation.
When the current module depends on other modules, the list of modules should
be added in the Makefile in the ``INCLUDE_DIRS`` variable.
Creating a new module
=====================
Every new module should be created using the interactive ``create_module.sh``
script located in the ``${QPACKAGE_ROOT}/scripts`` directory. This will create
all the required files with correct templates.
Makefiles
=========
Use the structure of Makefiles provided by the ``create_module.sh`` script. If
you need to re-create the Makefile, you can use the ``create_Makefile.sh``
script in the current module directory.
If you need to add some Fortran or C files that should not be tracked by IRPF90,
you have to add them manually to the Makefile in the ``SRC`` variable.
You also need to add the corresponding ``*.o`` file prefixed by ``IRPF90_temp/``.
For example
.. code-block:: Makefile
SRC=map_module.f90
OBJ=IRPF90_temp/map_module.o
Testing
=======
Each module contains a ``tests/`` directory which contains the test script.
Each module should be tested by running::
make test
Before merging into the master branch, the module should pass **all** the tests.
This enables the possibility to use ``git bisect`` to quickly find bugs.
Input data
==========
Every program is supposed to use an EZFIO database containing all the
persistent data. This database can be modified in using the generated Fortran
functions or the generated Python module.
The definition of the data needed by the module should be put in the
``*.ezfio_config`` file.
Input data can also be read from the standard input to enable the use of
a program with a pipe, but the read statements should be present **only** in
the main program.
Output data
===========
Print to stdout statements should only appear in programs, not in providers,
subroutines or functions. This enables the possibility easily use the programs
with pipes.
To print, you should write in an output file provided by the ``Output``
module.
Creating a shell script
=======================
Shell scripts should be located in the ``${QPACKAGE_ROOT}/scripts`` directory.
Relative paths should be avoided as much as possible, and the result of commands
should be always checked. For example, when creating a directory the existence
of the directory has to be checked.

4
src/Utils/Makefile
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@ -1,7 +1,7 @@
default: all
# Define here all other modules on which the current module depends
INCLUDE_DIRS =
NEEDED_MODULES=$(shell cat NEEDED_MODULES)
# Define here all new external source files and objects.Don't forget to prefix the
# object files with IRPF90_temp/
@ -13,7 +13,7 @@ include $(QPACKAGE_ROOT)/src/Makefile.config
include $(QPACKAGE_ROOT)/src/Makefile.common
include irpf90.make
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES
$(IRPF90)
Makefile.depend: Makefile

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@ -0,0 +1 @@

77
src/coding_rules.rst
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@ -1,77 +0,0 @@
======================
Programming guidelines
======================
Each module (directory) contains the following:
* A :file:`README.rst` file to document the current module.
* An :file:`ASSUMPTIONS.rst` file. This file should document all the implicit
assumptions used in the module. For example, if the atomic orbitals are
assumed to be normalized, this should be mentioned in the
:file:`AOs/ASSUMPTIONS.rst` file.
* A set of :file:`.irp.f` files containing provider, subroutines and functions
* A :file:`tests` directory that should contain the test programs of the module
(see testing section)
* A :file:`Makefile` that should compile
* Optionally some :file:`*.ezfio_config` configuration files for the EZFIO
library
A new module may be created by invoking the :file:`create_module.sh` script.
Every subroutine, function or provider should be documented using the
BEGIN_DOC ... END_DOC block. The documentation should be written in
ReStructured Text format to enable the automatic generation of the Sphinx
documentation.
Testing
=======
Each module contains a :file:`tests` directory which contains the test script.
Each module should be tested by running::
make test
Before merging into the master branch, the module should pass **all** the tests.
This enables the possibility tu use :command:`git bisect` to quickly find bugs.
Input data
==========
Every program is supposed to use an EZFIO database containing all the
persistent data. This database can be modified in using the generated Fortran
functions or the generated Python module.
The definition of the data needed by the module should be put in the
:file:`*.ezfio_config` file.
Input data can also be read from the standard input to enable the use of
a program with a pipe, but the read statements should be present **only** in
the main program.
Output data
===========
Print to stdout statements should only appear in programs, not in providers,
subroutines or functions. This enables the possibility easily use the programs
with pipes.
To print, you should write in an output file provided by the :file:`Output`
module.
Modifying MOs
=============
When modifying MOs, the label of the current MOs should change accordingly by changing the mo_label. For example:
.. code-block:: fortran
mo_coef = new_mo_coef
mo_label = "MyNewLabel"
TOUCH mo_coef mo_label