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mirror of https://github.com/LCPQ/quantum_package synced 2024-12-22 20:35:19 +01:00

Merge branch 'master' of github.com:scemama/quantum_package

Conflicts:
	scripts/ezfio_interface.py
	scripts/install_ocaml.sh
This commit is contained in:
Anthony Scemama 2015-03-26 01:02:12 +01:00
commit 951538a01d
11 changed files with 386 additions and 90 deletions

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@ -3,23 +3,40 @@
## Requirements
* curl
* wget
* m4
* GNU make
* Intel Fortran compiler
* Python
* Fortran compiler (ifort or gfortran are tested)
* Python >= 2.7
* Bash
By default, the Ocaml compiler will be installed in `$HOME/ocamlbrew`.
To install it somewhere else, set the `$OCAMLBREW_BASE` environment
variable to the required destination, for example:
## Standard installation
export OCAMLBREW_BASE=/usr/local/ocamlbrew
1) `./setup_environment.sh`
For more info about the Ocaml installation, check the ocamlbrew
website : https://github.com/hcarty/ocamlbrew
This command will download and install all the requirements.
Installing OCaml and the Core library may take somme time
(up to 20min on an old machine).
2) `source quantum_package.rc`
This file contains all the environement variables neeeded by the quantum package
both to compile and run. This should also be done before running calculations.
3) `cp ./src/Makefile.config.gfortran ./src/Makefile.config`
Create the ``Makefile.config`` which contains all the flags needed by the compiler.
The is also an example for the Intel Compiler (`Makefile.config.ifort`).
Edit this file and tune the flags as you want.
4) `make build`
It will compile all the executables and tools.
5) `make binary`
Optional. It will build a `tar.gz` file containing everything needed to run the quantum package on a
machine where you can't compile.
## Installing behind a firewall
@ -61,4 +78,3 @@ website : https://github.com/hcarty/ocamlbrew
ssh -fN -D 10000 user@external-server.com

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@ -1,8 +1,10 @@
Quantum package
===============
[![Build Status](https://travis-ci.org/LCPQ/quantum_package.svg?branch=master)](https://travis-ci.org/LCPQ/quantum_package)
[![Gitter](https://badges.gitter.im/Join Chat.svg)](https://gitter.im/LCPQ/quantum_package?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
Set of quantum chemistry programs and libraries.
For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>), or the [Install](INSTALL.md) file.

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@ -62,13 +62,13 @@ def get_type_dict():
# ~#~#~#~#~#~#~#~ #
fancy_type['integer'] = Type("int", "integer")
fancy_type['int' ] = Type("int", "integer")
fancy_type['int'] = Type("int", "integer")
fancy_type['float' ] = Type("float", "double precision")
fancy_type['float'] = Type("float", "double precision")
fancy_type['double precision'] = Type("float", "double precision")
fancy_type['logical'] = Type("bool", "logical")
fancy_type['bool' ] = Type("bool", "logical")
fancy_type['bool'] = Type("bool", "logical")
# ~#~#~#~#~#~#~#~ #
# q p _ t y p e s #
@ -92,18 +92,39 @@ def get_type_dict():
type_dict = get_type_dict()
def get_dict_config_file(config_file_path,folder):
def get_dict_config_file(config_file_path, module_lower):
"""
Read a ezfio.cfg
Return a dict d[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
Input:
config_file_path is the config file path
(for example FULL_PATH/EZFIO.cfg)
module_lower is the MODULE name lowered
(Ex fullci)
Return a dict d[provider_name] = {type,
doc,
ezfio_name,
ezfio_dir,
interface,
default}
Type : Is a fancy_type named typle who containt fortran and ocaml type
doc : Is the doc
ezfio_name : Will be the name of the file
ezfio_dir : Will be the folder who containt the ezfio_name
* /ezfio_dir/ezfio_name
* equal to MODULE_lower name for the moment.
interface : The provider is a imput or a output
if is a output:
default : The default value
"""
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
d = defaultdict(dict)
list_option_required = ["default", "doc"]
list_option = ["ezfio_name", "output"]
l_info_required = ["doc", "interface"]
l_info_optional = ["ezfio_name"]
# ~#~#~#~#~#~#~#~#~#~#~ #
# L o a d _ C o n f i g #
@ -116,43 +137,63 @@ def get_dict_config_file(config_file_path,folder):
# F i l l _ d i c t #
# ~#~#~#~#~#~#~#~#~ #
provider_names = config_file.sections()
for p in provider_names:
provider_name = p.lower()
default_d = {"ezfio_name": provider_name, "output": "false" }
def error(o, p, c):
"o option ; p provider_name ;c config_file_path"
print "You need a {0} for {1} in {2}".format(o, p, c)
for section in config_file.sections():
# pvd = provider
pvd = section.lower()
# Create the dictionary who containt the value per default
d_default = {"ezfio_name": pvd}
# Set the ezfio_dir
d[pvd]["ezfio_dir"] = module_lower
# Check if type if avalaible
type_ = config_file.get(p, "type")
type_ = config_file.get(section, "type")
if type_ not in type_dict:
print "{0} not avalaible. Choose in:".format(type_)
print ", ".join([i for i in type_dict])
sys.exit(1)
else:
d[provider_name]["type"] = type_dict[type_]
d[pvd]["type"] = type_dict[type_]
# Fill the dict with allother the information
for k in list_option_required:
# Fill the dict with REQUIRED information
for option in l_info_required:
try:
d[provider_name][k] = config_file.get(p, k)
d[pvd][option] = config_file.get(section, option)
except ConfigParser.NoOptionError:
print "You need a {0} for {1} in {2}".format(k,
provider_name,
config_file_path)
d[provider_name]["ezfio_dir"] = folder
for k in list_option:
try:
d[provider_name][k] = config_file.get(p, k).lower()
except ConfigParser.NoOptionError:
d[provider_name][k] = default_d[k]
error(option, pvd, config_file_path)
sys.exit(1)
# Convert string to bool
d[provider_name]["output"] = bool_convertor(d[provider_name]["output"])
# Fill the dict with OPTIONAL information
for option in l_info_optional:
try:
d[pvd][option] = config_file.get(section, option).lower()
except ConfigParser.NoOptionError:
d[pvd][option] = d_default[option]
# If interface is output we need a default value information
if d[pvd]["interface"] == "output":
try:
d[pvd]["default"] = config_file.get(section, "default")
except ConfigParser.NoOptionError:
error("default", pvd, config_file_path)
sys.exit(1)
return dict(d)
def create_ezfio_provider(dict_ezfio_cfg):
"""
From dict d[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
From dict d[provider_name] = {type,
doc,
ezfio_name,
ezfio_dir,
interface,
default}
create the a list who containt all the code for the provider
return [code, ...]
"""
@ -162,7 +203,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
ez_p = EZFIO_Provider()
for provider_name, dict_info in dict_ezfio_cfg.iteritems():
if not dict_info["output"]:
if "default" in dict_info:
ez_p.set_type(dict_info['type'].fortran)
ez_p.set_name(provider_name)
ez_p.set_doc(dict_info['doc'])
@ -178,8 +219,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
def save_ezfio_provider(path_head, dict_code_provider):
"""
Write in "ezfio_interface.irp.f" the
value of dict_code_provider
Write in path_head/"ezfio_interface.irp.f" the value of dict_code_provider
"""
path = "{0}/ezfio_interface.irp.f".format(path_head)
@ -206,30 +246,33 @@ def save_ezfio_provider(path_head, dict_code_provider):
f.write(output)
def create_ezfio_config(dict_ezfio_cfg, opt, folder):
def create_ezfio_config(dict_ezfio_cfg, opt, module_lower):
"""
From dict_ezfio_cfg[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
Return the string ezfio_interface_config
"""
result = [ folder ]
lenmax = max( [ len(i) for i in dict_ezfio_cfg ] )+2
result = [module_lower]
lenmax = max([len(i) for i in dict_ezfio_cfg]) + 2
l = sorted(dict_ezfio_cfg.keys())
for provider_name in l:
provider_info = dict_ezfio_cfg[provider_name]
s = " {0} {1}".format( provider_name.lower().ljust(lenmax), provider_info["type"].fortran )
result.append(s)
provider_info = dict_ezfio_cfg[provider_name]
s = " {0} {1}".format(
provider_name.lower().ljust(lenmax),
provider_info["type"].fortran)
result.append(s)
return "\n".join(result)
def save_ezfio_config(folder, str_ezfio_config):
def save_ezfio_config(module_lower, str_ezfio_config):
"""
Write the str_ezfio_config in
$QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(folder)
$QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
"""
ezfio_dir = "{0}/EZFIO".format(os.environ['QPACKAGE_ROOT'])
path = "{0}/config/{1}.ezfio_interface_config".format(ezfio_dir,
folder)
module_lower)
# print "Path = {}".format(path)
@ -245,27 +288,33 @@ def save_ezfio_config(folder, str_ezfio_config):
with open(path, "w") as f:
f.write(str_ezfio_config)
def main():
"""Take in argument a EZFIO.cfg"""
"""
Two condition:
-Take the EZFIO.cfg path in arg
or
-Look if EZFIO.cfg is present in the pwd
"""
try:
path = sys.argv[1]
config_file_path = sys.argv[1]
except:
path = "EZFIO.cfg"
if "EZFIO.cfg" not in os.listdir(os.getcwd()):
sys.exit(0)
config_file_path = "EZFIO.cfg"
if "EZFIO.cfg" not in os.listdir(os.getcwd()):
sys.exit(0)
path = os.path.expanduser(path)
path = os.path.expandvars(path)
path = os.path.abspath(path)
# print path
config_file_path = os.path.expanduser(config_file_path)
config_file_path = os.path.expandvars(config_file_path)
config_file_path = os.path.abspath(config_file_path)
# print config_file_path
path_dirname = os.path.dirname(path)
folder = [i for i in path_dirname.split("/") if i][-1]
folder = folder.lower()
path_dirname = os.path.dirname(config_file_path)
module = [i for i in path_dirname.split("/") if i][-1]
module_lower = module.lower()
# print "Found a EZFIO.cfg in {}".format(path)
dict_info_provider = get_dict_config_file(path,folder)
# print "Read {0}".format(config_file_path)
dict_info_provider = get_dict_config_file(config_file_path, module_lower)
# print "Generating the ezfio_interface.irp.f: \n"
d_config = create_ezfio_provider(dict_info_provider)
@ -274,12 +323,11 @@ def main():
save_ezfio_provider(path_dirname, d_config)
# print "Generating the ezfio_config"
config_ezfio = create_ezfio_config(dict_info_provider, "config", folder)
config_ezfio = create_ezfio_config(dict_info_provider, "config", module_lower)
# print "Saving ezfio_config"
save_ezfio_config(folder, config_ezfio)
save_ezfio_config(module_lower, config_ezfio)
if __name__ == "__main__":
main()
main()

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@ -24,6 +24,10 @@ skip
init_main
filter_integrals
filter2h2p
filterhole
filterparticle
do_double_excitations
check_double_excitation
""".split()
class H_apply(object):
@ -116,6 +120,24 @@ class H_apply(object):
buffer = buffer.replace('$'+key, value)
return buffer
def unset_double_excitations(self):
self["do_double_excitations"] = ".False."
self["check_double_excitation"] = """
check_double_excitation = .False.
"""
def set_filter_holes(self):
self["filterhole"] = """
if(iand(ibset(0_bit_kind,j),hole(k,other_spin)).eq.0_bit_kind )cycle
"""
def set_filter_particl(self):
self["filterparticle"] = """
if(iand(ibset(0_bit_kind,j_a),hole(k_a,other_spin)).eq.0_bit_kind )cycle
"""
def unset_skip(self):
self["skip"] = """
"""
def set_filter_2h_2p(self):
self["filter2h2p"] = """
! ! DIR$ FORCEINLINE

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@ -50,11 +50,12 @@ ${QPACKAGE_ROOT}/scripts/fetch_from_web.py \
chmod +x opam_installer.sh
echo N | ./opam_installer.sh ${QPACKAGE_ROOT}/bin
if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]; then
if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]
then
echo "Installation of OPAM failed"
exit 2
fi
rm opam_installer.sh
rm -f opam_installer.sh
${QPACKAGE_ROOT}/bin/opam config setup -a --dot-profile ${QPACKAGE_ROOT}/quantum_package.rc
source ${QPACKAGE_ROOT}/quantum_package.rc

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@ -23,7 +23,7 @@ EOF
gcc /tmp/main.c -lz
if [[ $? -eq 0 ]]
then
rm /tmp/main.c
rm /tmp/main.c "a.out"
exit 0
fi
rm /tmp/main.c

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@ -36,6 +36,11 @@ subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_gene
ifirst=1
endif
logical :: check_double_excitation
check_double_excitation = .True.
$initialization
$omp_parallel
@ -276,6 +281,12 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc $param
logical, allocatable :: array_pairs(:,:)
double precision :: diag_H_mat_elem
integer(omp_lock_kind), save :: lck, ifirst=0
logical :: check_double_excitation
check_double_excitation = .True.
$check_double_excitation
if (ifirst == 0) then
ifirst=1
!$ call omp_init_lock(lck)
@ -333,9 +344,11 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc $param
hole = key_in
k = ishft(i_a-1,-bit_kind_shift)+1
j = i_a-ishft(k-1,bit_kind_shift)-1
$filterhole
hole(k,ispin) = ibclr(hole(k,ispin),j)
k_a = ishft(j_a-1,-bit_kind_shift)+1
l_a = j_a-ishft(k_a-1,bit_kind_shift)-1
$filterparticle
hole(k_a,ispin) = ibset(hole(k_a,ispin),l_a)
$filter2h2p
key_idx += 1

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@ -1,37 +1,42 @@
[N_det_max_fci]
doc: Max number of determinants in the wave function
type: Det_number_max
doc: Max number of determinants in the wave function
interface: output
default: 10000
[N_det_max_fci_property]
doc: Max number of determinants in the wave function when you select for a given property
type: Det_number_max
doc: Max number of determinants in the wave function when you select for a given property
interface: output
default: 10000
[do_pt2_end]
type: logical
doc: If true, compute the PT2 at the end of the selection
interface: output
default: true
[PT2_max]
type: PT2_energy
doc: The selection process stops when the largest PT2 (for all the state is lower
than pt2_max in absolute value
interface: output
default: 0.0001
[var_pt2_ratio]
type: Normalized_float
doc: The selection process stops when the energy ratio variational/(variational+PT2)
is equal to var_pt2_ratio
interface: output
default: 0.75
[energy]
type: double precision
doc: "Calculated Full CI energy"
output: true
interface: input
[energy_pt2]
type: double precision
doc: "Calculated Full CI energy"
output: true
interface: input

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@ -10,23 +10,26 @@ s = H_apply("FCI_PT2")
s.set_perturbation("epstein_nesbet_2x2")
print s
s = H_apply("FCI_no_skip")
s.set_selection_pt2("epstein_nesbet_2x2")
s.unset_skip()
print s
if False:
s = H_apply("FCI_mono")
s.set_selection_pt2("epstein_nesbet_2x2")
s.unset_double_excitations()
print s
s = H_apply("FCI_mono")
s.set_selection_pt2("epstein_nesbet_2x2")
s.unset_double_excitations()
print s
s = H_apply("select_mono_delta_rho")
s.unset_double_excitations()
s.set_selection_pt2("delta_rho_one_point")
print s
s = H_apply("select_mono_delta_rho")
s.unset_double_excitations()
s.set_selection_pt2("delta_rho_one_point")
print s
s = H_apply("pt2_mono_delta_rho")
s.unset_double_excitations()
s.set_perturbation("delta_rho_one_point")
print s
s = H_apply("pt2_mono_delta_rho")
s.unset_double_excitations()
s.set_perturbation("delta_rho_one_point")
print s
s = H_apply("select_mono_di_delta_rho")
s.set_selection_pt2("delta_rho_one_point")

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@ -0,0 +1,91 @@
program full_ci
implicit none
integer :: i,k
double precision, allocatable :: pt2(:), norm_pert(:), H_pert_diag(:)
integer :: N_st, degree
N_st = N_states
allocate (pt2(N_st), norm_pert(N_st),H_pert_diag(N_st))
character*(64) :: perturbation
pt2 = 1.d0
diag_algorithm = "Lapack"
if (N_det > n_det_max_fci) then
call diagonalize_CI
call save_wavefunction
psi_det = psi_det_sorted
psi_coef = psi_coef_sorted
N_det = n_det_max_fci
soft_touch N_det psi_det psi_coef
call diagonalize_CI
call save_wavefunction
print *, 'N_det = ', N_det
print *, 'N_states = ', N_states
print *, 'PT2 = ', pt2
print *, 'E = ', CI_energy
print *, 'E+PT2 = ', CI_energy+pt2
print *, '-----'
endif
double precision :: i_H_psi_array(N_states),diag_H_mat_elem,h,i_O1_psi_array(N_states)
if(read_wf)then
call i_H_psi(psi_det(1,1,N_det),psi_det,psi_coef,N_int,N_det,psi_det_size,N_states,i_H_psi_array)
h = diag_H_mat_elem(psi_det(1,1,N_det),N_int)
selection_criterion = dabs(psi_coef(N_det,1) * (i_H_psi_array(1) - h * psi_coef(N_det,1))) * 0.1d0
soft_touch selection_criterion
endif
integer :: n_det_before
print*,'Beginning the selection ...'
do while (N_det < n_det_max_fci.and.maxval(abs(pt2(1:N_st))) > pt2_max)
n_det_before = N_det
call H_apply_FCI_no_skip(pt2, norm_pert, H_pert_diag, N_st)
PROVIDE psi_coef
PROVIDE psi_det
PROVIDE psi_det_sorted
if (N_det > n_det_max_fci) then
psi_det = psi_det_sorted
psi_coef = psi_coef_sorted
N_det = n_det_max_fci
soft_touch N_det psi_det psi_coef
endif
call diagonalize_CI
call save_wavefunction
if(n_det_before == N_det)then
selection_criterion = selection_criterion * 0.5d0
endif
print *, 'N_det = ', N_det
print *, 'N_states = ', N_states
print *, 'PT2 = ', pt2
print *, 'E = ', CI_energy
print *, 'E+PT2 = ', CI_energy+pt2
print *, '-----'
call ezfio_set_full_ci_energy(CI_energy)
if (abort_all) then
exit
endif
enddo
N_det = min(n_det_max_fci,N_det)
touch N_det psi_det psi_coef
call diagonalize_CI
if(do_pt2_end)then
print*,'Last iteration only to compute the PT2'
threshold_selectors = 1.d0
threshold_generators = 0.999d0
call H_apply_FCI_PT2(pt2, norm_pert, H_pert_diag, N_st)
print *, 'Final step'
print *, 'N_det = ', N_det
print *, 'N_states = ', N_states
print *, 'PT2 = ', pt2
print *, 'E = ', CI_energy
print *, 'E+PT2 = ', CI_energy+pt2
print *, '-----'
call ezfio_set_full_ci_energy_pt2(CI_energy+pt2)
endif
call save_wavefunction
deallocate(pt2,norm_pert)
end

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@ -11,6 +11,10 @@ module map_module
! as integer*2 and is found by applying the map_mask
! to the initial key. The element are found in the
! cache_map using a binary search
!
! When using the map_update subroutine to build the map,
! the map_unique subroutine
! should be called before getting data from the map.
use omp_lib
@ -433,6 +437,97 @@ call omp_unset_lock(map%lock)
end
subroutine map_update_verbose(map, key, value, sze, thr)
use map_module
implicit none
type (map_type), intent(inout) :: map
integer, intent(in) :: sze
integer(key_kind), intent(inout) :: key(sze)
real(integral_kind), intent(inout) :: value(sze)
real(integral_kind), intent(in) :: thr
integer :: i
integer(map_size_kind) :: idx_cache, idx_cache_new
integer(cache_map_size_kind) :: idx
integer :: sze2
integer(cache_key_kind) :: cache_key
integer(map_size_kind) :: n_elements_temp
type (cache_map_type) :: local_map
logical :: map_sorted
! do i = 1, sze
! print*,'value in map = ',value(i)
! enddo
sze2 = sze
map_sorted = .True.
n_elements_temp = 0_8
n_elements_temp = n_elements_temp + 1_8
do while (sze2>0)
i=1
do while (i<=sze)
if (key(i) /= 0_8) then
idx_cache = ishft(key(i),map_shift)
if (omp_test_lock(map%map(idx_cache)%lock)) then
local_map%key => map%map(idx_cache)%key
local_map%value => map%map(idx_cache)%value
local_map%sorted = map%map(idx_cache)%sorted
local_map%map_size = map%map(idx_cache)%map_size
local_map%n_elements = map%map(idx_cache)%n_elements
do
!DIR$ FORCEINLINE
call search_key_big_interval(key(i),local_map%key, local_map%n_elements, idx, 1, local_map%n_elements)
if (idx > 0_8) then
! print*,'AHAAH'
! print*,'local_map%value(idx) = ',local_map%value(idx)
local_map%value(idx) = local_map%value(idx) + value(i)
! print*,'not a new value !'
! print*,'local_map%value(idx) = ',local_map%value(idx)
else
! Assert that the map has a proper size
if (local_map%n_elements == local_map%map_size) then
call cache_map_unique(local_map)
call cache_map_reallocate(local_map, local_map%n_elements + local_map%n_elements)
call cache_map_shrink(local_map,thr)
endif
cache_key = iand(key(i),map_mask)
local_map%n_elements = local_map%n_elements + 1_8
local_map%value(local_map%n_elements) = value(i)
! print*,'new value !'
local_map%key(local_map%n_elements) = cache_key
local_map%sorted = .False.
n_elements_temp = n_elements_temp + 1_8
endif ! idx > 0
key(i) = 0_8
i = i+1
sze2 = sze2-1
if (i>sze) then
i=1
endif
if ( (ishft(key(i),map_shift) /= idx_cache).or.(key(i)==0_8)) then
exit
endif
enddo
map%map(idx_cache)%key => local_map%key
map%map(idx_cache)%value => local_map%value
map%map(idx_cache)%sorted = local_map%sorted
map%map(idx_cache)%n_elements = local_map%n_elements
map%map(idx_cache)%map_size = local_map%map_size
map_sorted = map_sorted .and. local_map%sorted
call omp_unset_lock(map%map(idx_cache)%lock)
endif ! omp_test_lock
else
i=i+1
endif ! key = 0
enddo ! i
enddo ! sze2 > 0
call omp_set_lock(map%lock)
map%n_elements = map%n_elements + n_elements_temp
map%sorted = map%sorted .and. map_sorted
call omp_unset_lock(map%lock)
end
subroutine map_append(map, key, value, sze)
use map_module
implicit none