diff --git a/INSTALL.rst b/INSTALL.rst index 80a6e3b1..099cd4b5 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -25,8 +25,8 @@ sets all the environment variables required for the normal operation of the Running this script will also tell you which external dependencies are missing and need to be installed. -When all dependencies have been installed, ( the :command:`configure` will tell you) -source the :file:`quantum_package.rc` in order to load all environment variables and compile the |QP|. +When all dependencies have been installed, ( the :command:`configure` will tell you) +source the :file:`quantum_package.rc` in order to load all environment variables and compile the |QP|. Requirements @@ -36,14 +36,14 @@ Requirements - Fortran compiler : GNU Fortran, Intel Fortran or IBM XL Fortran - `GNU make`_ - `Autoconf`_ -- `Python`_ > 2.6 +- `Python`_ > 3.0 - |IRPF90| : Fortran code generator - |EZFIO| : Easy Fortran Input/Output library generator - |BLAS| and |LAPACK| - `Zlib`_ - |ZeroMQ| : networking library - `GMP `_ : Gnu Multiple Precision Arithmetic Library -- |OCaml| compiler with |OPAM| package manager +- |OCaml| compiler with |OPAM| package manager - `Bubblewrap `_ : Sandboxing tool required by Opam - `libcap `_ : POSIX capabilities required by Bubblewrap - |Ninja| : a parallel build system @@ -83,29 +83,29 @@ spack install quantum_package Using the :command:`configure` executable ----------------------------------------- -The :command:`configure` executable can help you in installing the minimal dependencies you will need to compile the |QP|. -The command is to be used as follows: +The :command:`configure` executable can help you in installing the minimal dependencies you will need to compile the |QP|. +The command is to be used as follows: .. code:: bash ./configure --install -The following packages are supported by the :command:`configure` installer: +The following packages are supported by the :command:`configure` installer: -* ninja -* irpf90 -* zeromq +* ninja +* irpf90 +* zeromq * f77zmq * gmp * libcap * bwrap * ocaml ( :math:`\approx` 10 minutes) -* ezfio -* docopt -* resultsFile +* ezfio +* docopt +* resultsFile * bats -Example: +Example: .. code:: bash @@ -124,7 +124,7 @@ Example: If the :command:`configure` executable fails to install a specific dependency ----------------------------------------------------------------------------- -If the :command:`configure` executable does not succeed to install a specific dependency, +If the :command:`configure` executable does not succeed to install a specific dependency, there are some proposition of how to download and install the minimal dependencies to compile and use the |QP|. @@ -149,13 +149,13 @@ IRPF90 ------ *IRPF90* is a Fortran code generator for programming using the Implicit Reference -to Parameters (IRP) method. +to Parameters (IRP) method. -If you have *pip* for Python2, you can do +If you have *pip* for Python3, you can do .. code:: bash - python2 -m pip install --user irpf90 + python3 -m pip install --user irpf90 Otherwise, @@ -329,26 +329,26 @@ OCaml ``_ and move it in the :file:`${QP_ROOT}/external` directory -* If you use OCaml only with the |qp|, you can install the OPAM directory +* If you use OCaml only with the |qp|, you can install the OPAM directory containing the compiler and all the installed libraries in the :file:`${QP_ROOT}/external` directory as .. code:: bash - + export OPAMROOT=${QP_ROOT}/external/opam * Run the installer .. code:: bash - + echo ${QP_ROOT}/bin ${QP_ROOT}/external/opam_installer.sh --no-backup --fresh The :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin` directory. To do this, take the output of ``echo ${QP_ROOT}/bin`` and use it as an answer to where :command:`opam` should be installed. - + * Install the OCaml compiler @@ -387,11 +387,11 @@ Docopt *Docopt* is a Python package defining a command-line interface description language. -If you have *pip* for Python2, you can do +If you have *pip* for Python3, you can do .. code:: bash - python2 -m pip install --user docopt + python3 -m pip install --user docopt Otherwise, @@ -408,11 +408,11 @@ resultsFile *resultsFile* is a Python package to extract data from output files of quantum chemistry codes. -If you have *pip* for Python2, you can do +If you have *pip* for Python3, you can do .. code:: bash - python2 -m pip install --user resultsFile + python3 -m pip install --user resultsFile diff --git a/bin/qp_basis b/bin/qp_basis index 87a04ccc..8722205b 100755 --- a/bin/qp_basis +++ b/bin/qp_basis @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ @@ -12,7 +12,7 @@ Usage: """ -from __future__ import print_function + import sys import os import subprocess diff --git a/bin/qp_convert_output_to_ezfio b/bin/qp_convert_output_to_ezfio index 30faa686..5f0c4771 100755 --- a/bin/qp_convert_output_to_ezfio +++ b/bin/qp_convert_output_to_ezfio @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ convert output of GAMESS/GAU$$IAN to ezfio @@ -22,7 +22,7 @@ try: QP_ROOT = os.environ["QP_ROOT"] QP_EZFIO = os.environ["QP_EZFIO"] except KeyError: - print "Error: QP_ROOT environment variable not found." + print("Error: QP_ROOT environment variable not found.") sys.exit(1) else: sys.path = [QP_EZFIO + "/Python", @@ -30,10 +30,11 @@ else: QP_ROOT + "/install", QP_ROOT + "/scripts"] + sys.path +from resultsFile import * try: from resultsFile import * except: - print "Error: resultsFile Python library not installed" + print("Error: resultsFile Python library not installed") sys.exit(1) @@ -48,17 +49,17 @@ def write_ezfio(res, filename): # |_ | _ _ _|_ ._ _ ._ _ # |_ | (/_ (_ |_ | (_) | | _> # - print "Electrons\t...\t", + print("Electrons\t...\t", end=' ') ezfio.set_electrons_elec_alpha_num(res.num_alpha) ezfio.set_electrons_elec_beta_num(res.num_beta) - print "OK" + print("OK") # # |\ | _ | _ o # | \| |_| (_ | (/_ | # - print "Nuclei\t\t...\t", + print("Nuclei\t\t...\t", end=' ') # ~#~#~#~ # # I n i t # # ~#~#~#~ # @@ -93,24 +94,23 @@ def write_ezfio(res, filename): # Transformt H1 into H import re - p = re.compile(ur'(\d*)$') + p = re.compile(r'(\d*)$') label = [p.sub("", x.name).capitalize() for x in res.geometry] ezfio.set_nuclei_nucl_label(label) ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z) - print "OK" + print("OK") # _ # /\ _ _ |_) _. _ o _ # /--\ (_) _> |_) (_| _> | _> # - print "AOS\t\t...\t", + print("AOS\t\t...\t", end=' ') # ~#~#~#~ # # I n i t # # ~#~#~#~ # - import string at = [] num_prim = [] power_x = [] @@ -131,9 +131,9 @@ def write_ezfio(res, filename): at.append(i + 1) num_prim.append(len(b.prim)) s = b.sym - power_x.append(string.count(s, "x")) - power_y.append(string.count(s, "y")) - power_z.append(string.count(s, "z")) + power_x.append(str.count(s, "x")) + power_y.append(str.count(s, "y")) + power_z.append(str.count(s, "z")) coefficient.append(b.coef) exponent.append([p.expo for p in b.prim]) @@ -175,14 +175,14 @@ def write_ezfio(res, filename): ezfio.set_ao_basis_ao_expo(expo) ezfio.set_ao_basis_ao_basis("Read by resultsFile") - print "OK" + print("OK") # _ # |\/| _ _ |_) _. _ o _ # | | (_) _> |_) (_| _> | _> # - print "MOS\t\t...\t", + print("MOS\t\t...\t", end=' ') # ~#~#~#~ # # I n i t # # ~#~#~#~ # @@ -205,9 +205,9 @@ def write_ezfio(res, filename): virtual = [] active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))] - closed = map(lambda x: x[1], closed) - active = map(lambda x: x[1], active) - virtual = map(lambda x: x[1], virtual) + closed = [x[1] for x in closed] + active = [x[1] for x in active] + virtual = [x[1] for x in virtual] MOindices = closed + active + virtual MOs = [] @@ -223,7 +223,7 @@ def write_ezfio(res, filename): MOmap[i] = MOindices.index(i) energies = [] - for i in xrange(mo_num): + for i in range(mo_num): energies.append(MOs[i].eigenvalue) if res.occ_num is not None: @@ -237,11 +237,11 @@ def write_ezfio(res, filename): MoMatrix = [] sym0 = [i.sym for i in res.mo_sets[MO_type]] sym = [i.sym for i in res.mo_sets[MO_type]] - for i in xrange(len(sym)): + for i in range(len(sym)): sym[MOmap[i]] = sym0[i] MoMatrix = [] - for i in xrange(len(MOs)): + for i in range(len(MOs)): m = MOs[i] for coef in m.vector: MoMatrix.append(coef) @@ -256,10 +256,10 @@ def write_ezfio(res, filename): ezfio.set_mo_basis_mo_num(mo_num) ezfio.set_mo_basis_mo_occ(OccNum) ezfio.set_mo_basis_mo_coef(MoMatrix) - print "OK" + print("OK") - print "Pseudos\t\t...\t", + print("Pseudos\t\t...\t", end=' ') try: lmax = 0 nucl_charge_remove = [] @@ -327,7 +327,7 @@ def write_ezfio(res, filename): else: ezfio.set_pseudo_do_pseudo(True) - print "OK" + print("OK") @@ -354,15 +354,15 @@ if __name__ == '__main__': except: raise else: - print FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0] + print(FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0]) write_ezfio(RES_FILE, EZFIO_FILE) sys.stdout.flush() if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0: - print """Warning: You need to run + print("""Warning: You need to run qp run save_ortho_mos to be sure your MOs will be orthogonal, which is not the case when -the MOs are read from output files (not enough precision in output).""" +the MOs are read from output files (not enough precision in output).""") diff --git a/bin/qp_name b/bin/qp_name index f0551652..d15e16d0 100755 --- a/bin/qp_name +++ b/bin/qp_name @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ Displays the names of all the files in which the provider/subroutine/function @@ -30,7 +30,7 @@ try: from docopt import docopt from qp_path import QP_SRC, QP_ROOT except ImportError: - print "source .quantum_package.rc" + print("source .quantum_package.rc") raise @@ -38,7 +38,7 @@ def main(arguments): """Main function""" # Check that name exist in */IRPF90_man - print "Checking that name exists..." + print("Checking that name exists...") all_modules = os.listdir(QP_SRC) f = arguments[""]+".l" @@ -52,21 +52,21 @@ def main(arguments): if found: break if not found: - print "Error:" - print "The variable/subroutine/function \""+arguments[""] \ - + "\" was not found in the sources." - print "Did you compile the code at the root?" - print "Continue? [y/N] ", + print("Error:") + print("The variable/subroutine/function \""+arguments[""] \ + + "\" was not found in the sources.") + print("Did you compile the code at the root?") + print("Continue? [y/N] ", end=' ') cont = sys.stdin.read(1).strip() in ["y", "Y"] if not cont: - print "Aborted" + print("Aborted") sys.exit(1) # Now search in all the files if arguments["--rename"]: - print "Replacing..." + print("Replacing...") else: - print "Searching..." + print("Searching...") name = re.compile(r"\b"+arguments[""]+r"\b", re.IGNORECASE) @@ -84,15 +84,15 @@ def main(arguments): with open(filename, "r") as f: f_in = f.read() if name.search(f_in): - print filename + print(filename) if arguments["--rename"]: f_new = name.sub(arguments["--rename"], f_in) with open(filename, "w") as f: f.write(f_new) - print "Done" + print("Done") with open(os.path.join(QP_ROOT, "REPLACE"), 'a') as f: - print >>f, "qp_name "+" ".join(sys.argv[1:]) + print("qp_name "+" ".join(sys.argv[1:]), file=f) diff --git a/bin/qp_plugins b/bin/qp_plugins index b32f907f..ef0f5a45 100755 --- a/bin/qp_plugins +++ b/bin/qp_plugins @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Usage: @@ -43,9 +43,9 @@ try: from module_handler import get_l_module_descendant from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT except ImportError: - print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" - print "(`source ${QP_ROOT}/quantum_package.rc`)" - print sys.exit(1) + print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc") + print("(`source ${QP_ROOT}/quantum_package.rc`)") + print(sys.exit(1)) def save_new_module(path, l_child): @@ -58,7 +58,7 @@ def save_new_module(path, l_child): try: os.makedirs(path) except OSError: - print "The module ({0}) already exists...".format(path) + print("The module ({0}) already exists...".format(path)) sys.exit(1) with open(os.path.join(path, "NEED"), "w") as f: @@ -105,7 +105,7 @@ def main(arguments): if arguments["list"]: if arguments["--repositories"]: for repo in get_repositories(): - print repo + print(repo) else: # Search in QP_PLUGINS all directories with a NEED file @@ -121,7 +121,7 @@ def main(arguments): for (x, y) in l_tmp: d_tmp[x] = y repo_of_plugin[y] = x.replace(QP_PLUGINS+'/','') - l_repository = d_tmp.keys() + l_repository = list(d_tmp.keys()) if l_repository == []: l_result = [] else: @@ -142,7 +142,7 @@ def main(arguments): l_result = [f for f in l_plugins if f not in l_installed] for module in sorted(l_result): - print "%-30s %-30s"%(module, repo_of_plugin[module]) + print("%-30s %-30s"%(module, repo_of_plugin[module])) if arguments["create"]: @@ -159,29 +159,29 @@ def main(arguments): path = os.path.join(QP_PLUGINS, repository, name) - print "Created plugin:" - print path, '\n' + print("Created plugin:") + print(path, '\n') for children in l_children: if children not in m_instance.dict_descendant: - print "Error: {0} is not a valid module.".format(children) + print("Error: {0} is not a valid module.".format(children)) sys.exit(1) - print "Needed modules:" - print l_children, '\n' + print("Needed modules:") + print(l_children, '\n') - print "This corresponds to using the following modules:" - print l_children + m_instance.l_descendant_unique(l_children), '\n' + print("This corresponds to using the following modules:") + print(l_children + m_instance.l_descendant_unique(l_children), '\n') - print "Which is reduced to:" + print("Which is reduced to:") l_child_reduce = m_instance.l_reduce_tree(l_children) - print l_child_reduce, '\n' + print(l_child_reduce, '\n') - print "Installation", + print("Installation", end=' ') save_new_module(path, l_child_reduce) - print " [ OK ]" - print "" + print(" [ OK ]") + print("") arguments["create"] = False arguments["install"] = True main(arguments) @@ -228,7 +228,7 @@ def main(arguments): for (x, y) in [os.path.split(f) for f in l_tmp]: d_repo_of_plugin[y] = x d_repo[x] = None - l_repository = d_repo.keys() + l_repository = list(d_repo.keys()) d_plugin = get_dict_child(l_repository) @@ -236,7 +236,7 @@ def main(arguments): d_child.update(d_plugin) normalize_case = {} - for name in d_local.keys() + d_plugin.keys(): + for name in list(d_local.keys()) + list(d_plugin.keys()): normalize_case[name.lower()] = name l_name = [normalize_case[name.lower()] for name in arguments[""]] @@ -244,7 +244,7 @@ def main(arguments): for name in l_name: if name in d_local: - print "{0} Is already installed".format(name) + print("{0} Is already installed".format(name)) l_module_descendant = get_l_module_descendant(d_child, l_name) @@ -252,10 +252,10 @@ def main(arguments): if l_module_to_cp: - print "Required dependencies:" - print l_module_to_cp + print("Required dependencies:") + print(l_module_to_cp) - print "Installation...", + print("Installation...", end=' ') for module_to_cp in l_module_to_cp: src = os.path.join(d_repo_of_plugin[module_to_cp], module_to_cp) @@ -269,10 +269,10 @@ def main(arguments): subprocess.check_call([install]) os.chdir(wd) except OSError: - print "The src directory is broken. Please remove %s" % des + print("The src directory is broken. Please remove %s" % des) raise subprocess.check_call(["qp_create_ninja", "update"]) - print "[ OK ]" + print("[ OK ]") elif arguments["uninstall"]: @@ -285,17 +285,17 @@ def main(arguments): l_failed = [name for name in l_name if name not in d_local] if l_failed: - print "Plugins not installed:" + print("Plugins not installed:") for name in sorted(l_failed): - print "%s" % name + print("%s" % name) sys.exit(1) l_name_to_remove = l_name + \ [module for module in m_instance.l_module \ for name in l_name if name in d_descendant[module]] - print "Removing plugins:" - print l_name_to_remove + print("Removing plugins:") + print(l_name_to_remove) for module in set(l_name_to_remove): @@ -310,7 +310,7 @@ def main(arguments): try: os.unlink(os.path.join(QP_SRC, module)) except OSError: - print "%s is a core module which can't be removed" % module + print("%s is a core module which can't be removed" % module) elif arguments["update"]: @@ -321,7 +321,7 @@ def main(arguments): l_repositories = get_repositories() for repo in l_repositories: - print "Updating ", repo + print("Updating ", repo) os.chdir(os.path.join(QP_PLUGINS,repo)) git_cmd=["git", "pull"] subprocess.check_call(git_cmd) diff --git a/bin/qp_reset b/bin/qp_reset index b8c07adf..59646835 100755 --- a/bin/qp_reset +++ b/bin/qp_reset @@ -95,6 +95,7 @@ qp set_file $ezfio if [[ $dets -eq 1 ]] ; then rm --force -- ${ezfio}/determinants/n_det rm --force -- ${ezfio}/determinants/psi_{det,coef}.gz + rm --force -- ${ezfio}/determinants/psi_{det,coef}_qp_edit.gz fi if [[ $mos -eq 1 ]] ; then diff --git a/bin/qp_set_frozen_core b/bin/qp_set_frozen_core index 25b450dd..b00797e2 100755 --- a/bin/qp_set_frozen_core +++ b/bin/qp_set_frozen_core @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ @@ -49,7 +49,7 @@ import os.path try: import qp_path except ImportError: - print "source .quantum_package.rc" + print("source .quantum_package.rc") raise from docopt import docopt @@ -102,7 +102,7 @@ def main(arguments): mo_num = ezfio.mo_basis_mo_num if arguments["--query"]: - print n_frozen + print(n_frozen) sys.exit(0) if n_frozen == 0: diff --git a/bin/qp_set_frozen_large_core b/bin/qp_set_frozen_large_core index cce5ca70..6950b90c 100755 --- a/bin/qp_set_frozen_large_core +++ b/bin/qp_set_frozen_large_core @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ @@ -23,7 +23,7 @@ import os.path try: import qp_path except ImportError: - print "source .quantum_package.rc" + print("source .quantum_package.rc") raise from docopt import docopt @@ -62,7 +62,7 @@ def main(arguments): mo_num = ezfio.mo_basis_mo_num if arguments["--query"]: - print n_frozen + print(n_frozen) sys.exit(0) if n_frozen == 0: diff --git a/bin/qp_test b/bin/qp_test index e1730cc8..67b3ea02 100755 --- a/bin/qp_test +++ b/bin/qp_test @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ @@ -21,8 +21,8 @@ try: from docopt import docopt from qp_path import QP_SRC, QP_TESTS except ImportError: - print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" - print "(`source ${QP_ROOT}/quantum_package.rc`)" + print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc") + print("(`source ${QP_ROOT}/quantum_package.rc`)") sys.exit(1) @@ -54,11 +54,11 @@ def main(arguments): os.chdir(QP_TESTS) for bats_file in l_bats: - print "" - print "-~-~-~-~-~-~" - print "" - print "Running tests for %s"%(bats_file) - print "" + print("") + print("-~-~-~-~-~-~") + print("") + print("Running tests for %s"%(bats_file)) + print("") if arguments["-v"]: p = None if arguments["TEST"]: @@ -66,7 +66,7 @@ def main(arguments): else: test = "" try: - os.system(test+" python2 bats_to_sh.py "+bats_file+ + os.system(test+" python3 bats_to_sh.py "+bats_file+ "| bash") except: if p: diff --git a/config/ifort_avx.cfg b/config/ifort_avx.cfg index d3fcd1f0..25bf35eb 100644 --- a/config/ifort_avx.cfg +++ b/config/ifort_avx.cfg @@ -9,14 +9,14 @@ FC : ifort -fpic LAPACK_LIB : -mkl=parallel IRPF90 : irpf90 -IRPF90_FLAGS : --ninja --align=32 +IRPF90_FLAGS : --ninja --align=32 # Global options ################ # # 1 : Activate # 0 : Deactivate -# +# [OPTION] MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below CACHE : 0 ; Enable cache_compile.py @@ -32,14 +32,14 @@ OPENMP : 1 ; Append OpenMP flags # [OPT] FC : -traceback -FCFLAGS : -xAVX -O2 -ip -ftz -g +FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g # Profiling flags ################# # [PROFILE] FC : -p -g -FCFLAGS : -xSSE4.2 -O2 -ip -ftz +FCFLAGS : -xSSE4.2 -O2 -ip -ftz # Debugging flags ################# diff --git a/config/ifort_avx_mpi.cfg b/config/ifort_avx_mpi.cfg index 550dbf91..9a839e66 100644 --- a/config/ifort_avx_mpi.cfg +++ b/config/ifort_avx_mpi.cfg @@ -9,14 +9,14 @@ FC : mpiifort -fpic LAPACK_LIB : -mkl=parallel IRPF90 : irpf90 -IRPF90_FLAGS : --ninja --align=32 -DMPI +IRPF90_FLAGS : --ninja --align=32 -DMPI # Global options ################ # # 1 : Activate # 0 : Deactivate -# +# [OPTION] MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below CACHE : 0 ; Enable cache_compile.py @@ -31,14 +31,14 @@ OPENMP : 1 ; Append OpenMP flags # -ftz : Flushes denormal results to zero # [OPT] -FCFLAGS : -march=corei7-avx -O2 -ip -ftz -g -traceback +FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g -traceback # Profiling flags ################# # [PROFILE] FC : -p -g -FCFLAGS : -march=corei7 -O2 -ip -ftz +FCFLAGS : -march=corei7 -O2 -ip -ftz # Debugging flags diff --git a/config/ifort_debug.cfg b/config/ifort_debug.cfg index 32e4d895..f0f90f34 100644 --- a/config/ifort_debug.cfg +++ b/config/ifort_debug.cfg @@ -32,7 +32,7 @@ OPENMP : 1 ; Append OpenMP flags # [OPT] FC : -traceback -FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g +FCFLAGS : -msse4.2 -O2 -ip -ftz -g # Profiling flags @@ -40,7 +40,7 @@ FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g # [PROFILE] FC : -p -g -FCFLAGS : -xSSE4.2 -O2 -ip -ftz +FCFLAGS : -msse4.2 -O2 -ip -ftz # Debugging flags @@ -50,11 +50,11 @@ FCFLAGS : -xSSE4.2 -O2 -ip -ftz # -fpe0 : All floating point exaceptions # -C : Checks uninitialized variables, array subscripts, etc... # -g : Extra debugging information -# -xSSE2 : Valgrind needs a very simple x86 executable +# -msse4.2 : Valgrind needs a very simple x86 executable # [DEBUG] FC : -g -traceback -FCFLAGS : -xSSE4.2 -C -fpe0 -implicitnone +FCFLAGS : -msse4.2 -C -fpe0 -implicitnone # OpenMP flags diff --git a/config/ifort_epyc.cfg b/config/ifort_epyc.cfg deleted file mode 100644 index 1b2427de..00000000 --- a/config/ifort_epyc.cfg +++ /dev/null @@ -1,63 +0,0 @@ -# Common flags -############## -# -# -mkl=[parallel|sequential] : Use the MKL library -# --ninja : Allow the utilisation of ninja. It is mandatory ! -# --align=32 : Align all provided arrays on a 32-byte boundary -# -[COMMON] -FC : ifort -fpic -LAPACK_LIB : -mkl=parallel -IRPF90 : irpf90 -IRPF90_FLAGS : --ninja --align=32 - -# Global options -################ -# -# 1 : Activate -# 0 : Deactivate -# -[OPTION] -MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below -CACHE : 0 ; Enable cache_compile.py -OPENMP : 1 ; Append OpenMP flags - -# Optimization flags -#################### -# -# -xHost : Compile a binary optimized for the current architecture -# -O2 : O3 not better than O2. -# -ip : Inter-procedural optimizations -# -ftz : Flushes denormal results to zero -# -[OPT] -FC : -traceback -FCFLAGS : -march=core-avx2 -O2 -ip -ftz -g - -# Profiling flags -################# -# -[PROFILE] -FC : -p -g -FCFLAGS : -march=core-avx2 -O2 -ip -ftz - -# Debugging flags -################# -# -# -traceback : Activate backtrace on runtime -# -fpe0 : All floating point exaceptions -# -C : Checks uninitialized variables, array subscripts, etc... -# -g : Extra debugging information -# -xSSE2 : Valgrind needs a very simple x86 executable -# -[DEBUG] -FC : -g -traceback -FCFLAGS : -xSSE2 -C -fpe0 -implicitnone - -# OpenMP flags -################# -# -[OPENMP] -FC : -qopenmp -IRPF90_FLAGS : --openmp - diff --git a/config/ifort_mpi.cfg b/config/ifort_mpi.cfg index 5c3b1782..57087847 100644 --- a/config/ifort_mpi.cfg +++ b/config/ifort_mpi.cfg @@ -9,14 +9,14 @@ FC : mpiifort -fpic LAPACK_LIB : -mkl=parallel IRPF90 : irpf90 -IRPF90_FLAGS : --ninja --align=32 -DMPI +IRPF90_FLAGS : --ninja --align=32 -DMPI # Global options ################ # # 1 : Activate # 0 : Deactivate -# +# [OPTION] MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below CACHE : 0 ; Enable cache_compile.py @@ -31,14 +31,14 @@ OPENMP : 1 ; Append OpenMP flags # -ftz : Flushes denormal results to zero # [OPT] -FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g -traceback +FCFLAGS : -msse4.2 -O2 -ip -ftz -g -traceback # Profiling flags ################# # [PROFILE] FC : -p -g -FCFLAGS : -xSSE4.2 -O2 -ip -ftz +FCFLAGS : -msse4.2 -O2 -ip -ftz # Debugging flags diff --git a/configure b/configure index 5b9cf502..263ef926 100755 --- a/configure +++ b/configure @@ -3,7 +3,7 @@ # Quantum Package configuration script # -EZFIO_TGZ="EZFIO.1.6.2.tar.gz" +EZFIO_TGZ="EZFIO.2.0.2.tar.gz" @@ -315,3 +315,4 @@ fi exit 0 + diff --git a/docs/Makefile b/docs/Makefile index 7f886cbc..8ec191fc 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -14,7 +14,7 @@ help: .PHONY: help Makefile auto auto: - cd source ; python2 auto_generate.py + cd source ; python3 auto_generate.py # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). diff --git a/docs/source/auto_generate.py b/docs/source/auto_generate.py index a4dd32ca..11029c3b 100755 --- a/docs/source/auto_generate.py +++ b/docs/source/auto_generate.py @@ -1,9 +1,9 @@ #!/usr/bin/env python2 -from __future__ import print_function + import os import sys -import ConfigParser +import configparser from module_handler import get_binaries @@ -27,7 +27,7 @@ def generate_modules(abs_module, entities): EZFIO = os.path.join(abs_module,'EZFIO.cfg') if os.path.exists(EZFIO): rst += ["", "EZFIO parameters", "----------------", ""] - config_file = ConfigParser.ConfigParser() + config_file = configparser.ConfigParser() with open(EZFIO, 'r') as f: config_file.readfp(f) for section in config_file.sections(): diff --git a/etc/irpf90.rc b/etc/irpf90.rc index 05420e05..3bf2f2d7 100644 --- a/etc/irpf90.rc +++ b/etc/irpf90.rc @@ -18,10 +18,10 @@ function source_if_exists() { if [[ -f $1 ]]; then cd $(dirname $1) ; source $(basename $1) ; cd - fi &> /dev/null -} +} source ${QP_ROOT}/etc/autocomplete.rc source_if_exists "${IRPF90_PATH}/irpman-completions.bash" - + diff --git a/etc/paths.rc b/etc/paths.rc index ce82358a..366286d7 100644 --- a/etc/paths.rc +++ b/etc/paths.rc @@ -38,5 +38,6 @@ export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib) export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64) export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include) +export CPATH=$(qp_prepend_export "CPATH" "${QP_ROOT}"/include) diff --git a/external/EZFIO.1.6.2.tar.gz b/external/EZFIO.1.6.2.tar.gz deleted file mode 100644 index f364f88f..00000000 Binary files a/external/EZFIO.1.6.2.tar.gz and /dev/null differ diff --git a/external/EZFIO.2.0.2.tar.gz b/external/EZFIO.2.0.2.tar.gz new file mode 100644 index 00000000..3d1e7d75 Binary files /dev/null and b/external/EZFIO.2.0.2.tar.gz differ diff --git a/external/Python/.gitignore b/external/Python/.gitignore index e69de29b..1cd79fd6 100644 --- a/external/Python/.gitignore +++ b/external/Python/.gitignore @@ -0,0 +1,46 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.cache +nosetests.xml +coverage.xml + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ diff --git a/ocaml/qp_tunnel.ml b/ocaml/qp_tunnel.ml index 6669da06..84e50eb5 100644 --- a/ocaml/qp_tunnel.ml +++ b/ocaml/qp_tunnel.ml @@ -21,10 +21,6 @@ let () = doc="Downloads the EZFIO directory." ; arg=Without_arg; } ; - { short='v' ; long="verbose" ; opt=Optional ; - doc="Prints the transfer speed." ; - arg=Without_arg; } ; - anonymous "(EZFIO_DIR|ADDRESS)" Mandatory @@ -150,45 +146,6 @@ let () = Zmq.Socket.subscribe socket_in ""; - (* - let action = - if verbose then - begin - match req_or_sub with - | REQ -> (fun () -> - let msg = - Zmq.Socket.recv_all socket_in - in - let t0 = Unix.gettimeofday () in - Zmq.Socket.send_all socket_out msg; - let in_size = - float_of_int ( List.fold_left (fun accu x -> accu + String.length x) 0 msg ) - /. 8192. /. 1024. - in - let msg = - Zmq.Socket.recv_all socket_out - in - let t1 = Unix.gettimeofday () in - Zmq.Socket.send_all socket_in msg; - let in_time = t1 -. t0 in - in_time_sum := !in_time_sum +. in_time; - in_size_sum := !in_size_sum +. in_size; - Printf.printf " %16.2f MiB/s -- %16.2f MiB/s\n%!" (in_size /. in_time) (!in_size_sum /. !in_time_sum); - ) - | SUB -> (fun () -> - Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out) - end - else - begin - match req_or_sub with - | REQ -> (fun () -> - Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out; - Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in ) - | SUB -> (fun () -> - Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out) - end - in - *) let action_in = match req_or_sub with diff --git a/ocaml/qptypes_generator.ml b/ocaml/qptypes_generator.ml index 2c54a218..ce99fc78 100644 --- a/ocaml/qptypes_generator.ml +++ b/ocaml/qptypes_generator.ml @@ -219,22 +219,19 @@ module Perturbation : sig end = struct type t = | EN - | Barycentric - | Variance + | HF | SOP [@@deriving sexp] let to_string = function | EN -> \"EN\" - | Variance -> \"Variance\" - | Barycentric -> \"Barycentric\" + | HF -> \"HF\" | SOP -> \"SOP\" let of_string s = match (String.lowercase_ascii s) with | \"sop\" -> SOP | \"en\" -> EN - | \"variance\" -> Variance - | \"barycentric\" -> Barycentric + | \"hf\" -> HF | _ -> raise (Invalid_argument (\"Wrong Perturbation type : \"^s)) end " diff --git a/scripts/compilation/cache_compile.py b/scripts/compilation/cache_compile.py index d95adbda..440f6498 100755 --- a/scripts/compilation/cache_compile.py +++ b/scripts/compilation/cache_compile.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ Save the .o from a .f90 and is the .o is asked a second time, retur it @@ -13,9 +13,9 @@ import re import shutil import subprocess -r = re.compile(ur'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)') -p = re.compile(ur'-I IRPF90_temp/\S*\s+') -mod = re.compile(ur'module\s+(?P\S+).+end\s?module\s+(?P=mod)?', +r = re.compile(r'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)') +p = re.compile(r'-I IRPF90_temp/\S*\s+') +mod = re.compile(r'module\s+(?P\S+).+end\s?module\s+(?P=mod)?', re.MULTILINE | re.IGNORECASE) tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm") diff --git a/scripts/compilation/qp_create_ninja b/scripts/compilation/qp_create_ninja index 8381d1a2..3d4e56dc 100755 --- a/scripts/compilation/qp_create_ninja +++ b/scripts/compilation/qp_create_ninja @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Usage: qp_create_ninja create (--development | --production) @@ -24,7 +24,7 @@ except ImportError: "..", "quantum_package.rc")) - print "\n".join(["", "Error:", "source %s" % f, ""]) + print("\n".join(["", "Error:", "source %s" % f, ""])) sys.exit(1) # Compress path @@ -124,7 +124,7 @@ def dict_module_genelogy_path(d_module_genelogy): d_module_genelogy """ d = dict() - for module_rel, l_children_rel in d_module_genelogy.iteritems(): + for module_rel, l_children_rel in d_module_genelogy.items(): module_abs = real_join(QP_SRC, module_rel) p = Path(module_abs, module_rel) @@ -235,11 +235,11 @@ def ninja_ezfio_cfg_build(l_util): """ l_string = [] - for m in l_util.itervalues(): + for m in l_util.values(): str_ = "build {1} {2}: build_ezfio_interface {0}" - l_string += [str_.format(*map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs, - m.ez_config.abs)))] + l_string += [str_.format(*list(map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs, + m.ez_config.abs))))] l_string += [" sub_module = {0}".format(comp_path(m.ez_module.abs))] l_string += [""] @@ -257,8 +257,8 @@ def ninja_ezfio_config_build(l_ezfio_config): file_source = m.path_in_module file_create = m.path_in_ezfio - l_string += ["build {0}: build_ezfio_config {1}".format(*map(comp_path,(file_create, - file_source)))] + l_string += ["build {0}: build_ezfio_config {1}".format(*list(map(comp_path,(file_create, + file_source))))] l_string += [""] return l_string @@ -291,7 +291,7 @@ def ninja_ezfio_build(l_ezfio_config, l_util): """ l_ezfio_config = [i.path_in_ezfio for i in l_ezfio_config] - l_ezfio_from_cfg = [i.ez_config.abs for i in l_util.itervalues()] + l_ezfio_from_cfg = [i.ez_config.abs for i in l_util.values()] str_ = " ".join(map(comp_path,(l_ezfio_config + l_ezfio_from_cfg))) l_string = ["build {0}: build_ezfio {1}".format(EZFIO_LIB, str_), ""] @@ -335,7 +335,7 @@ def ninja_symlink_build(path_module, l_symlink): ""] for symlink in l_symlink: - l_string += ["build {0}: build_symlink {1}".format(*map(comp_path,(symlink.destination, symlink.source))), ""] + l_string += ["build {0}: build_symlink {1}".format(*list(map(comp_path,(symlink.destination, symlink.source)))), ""] return l_string @@ -360,7 +360,7 @@ def ninja_gitignore_build(path_module, d_binaries, l_symlink): path_gitignore = comp_path(join(path_module.abs, ".gitignore")) - l_b = map(comp_path,[i.abs for i in d_binaries[path_module]]) + l_b = list(map(comp_path,[i.abs for i in d_binaries[path_module]])) root = "build {0}: build_gitignore {1}".format(path_gitignore, " ".join(l_b)) @@ -420,9 +420,9 @@ def get_file_dependency(d_info_module): """ d_irp = defaultdict(dict) - for module, l_children in d_info_module.iteritems(): + for module, l_children in d_info_module.items(): - for key, values in get_l_file_for_module(module).iteritems(): + for key, values in get_l_file_for_module(module).items(): if key in ["l_src"]: values = [join(module.abs, o) for o in values] if key in ["l_obj"]: @@ -431,7 +431,7 @@ def get_file_dependency(d_info_module): d_irp[module][key] = values for children in l_children: - for key, values in get_l_file_for_module(children).iteritems(): + for key, values in get_l_file_for_module(children).items(): if key in ["l_src"]: values = [join(module.abs, children.rel, o) for o in values] @@ -495,10 +495,10 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp): # D e p e n d a n c y # # ~#~#~#~#~#~#~#~#~#~ # - l_depend = map(comp_path,d_irp[path_module]["l_depend"]) - l_src = map(comp_path,d_irp[path_module]["l_src"]) - l_obj = map(comp_path,d_irp[path_module]["l_obj"]) - l_template = map(comp_path,d_irp[path_module]["l_template"]) + l_depend = list(map(comp_path,d_irp[path_module]["l_depend"])) + l_src = list(map(comp_path,d_irp[path_module]["l_src"])) + l_obj = list(map(comp_path,d_irp[path_module]["l_obj"])) + l_template = list(map(comp_path,d_irp[path_module]["l_template"])) if l_needed_molule: l_symlink = ["l_symlink_{0}".format(path_module.rel)] @@ -511,7 +511,7 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp): # N i n j a _ b u i l d # # ~#~#~#~#~#~#~#~#~#~#~ # - l_include_dir = ["-I {0}".format(m.rel) for m in l_needed_molule] + l_include_dir = ["-I {0}".format(m.rel) for m in l_needed_molule] l_string = [ "build {0}: build_irpf90.ninja {1}".format(str_creation, str_depend), @@ -544,6 +544,7 @@ def get_binaries(path_module): stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = process.communicate() + stdout = stdout.decode() except OSError: return [] else: @@ -641,7 +642,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries): # ~#~#~ # ninja_module_path = join(comp_path(path_module.abs), "IRPF90_temp/build.ninja") - l_abs_bin = map(comp_path,[binary.abs for binary in d_binaries[path_module]]) + l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]])) # ~#~#~#~#~#~ # # s t r i n g # @@ -658,7 +659,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries): def ninja_module_build(path_module, d_binaries): - l_abs_bin = map(comp_path,[binary.abs for binary in d_binaries[path_module]]) + l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]])) path_readme = os.path.join(comp_path(path_module.abs), "README.rst") @@ -829,14 +830,14 @@ if __name__ == "__main__": dict_root = module_instance.dict_root dict_root_path = dict_module_genelogy_path(dict_root) - l_all_module = d_genealogy_path.keys() + l_all_module = list(d_genealogy_path.keys()) # ~#~#~#~#~#~#~#~#~#~#~#~#~ # # M o d u l e _ t o _ i r p # # ~#~#~#~#~#~#~#~#~#~#~#~#~ # d_binaries = get_dict_binaries(l_all_module, mode="development") - l_module = d_binaries.keys() + l_module = list(d_binaries.keys()) # ~#~#~#~#~#~#~#~#~#~#~#~ # diff --git a/scripts/compilation/read_compilation_cfg.py b/scripts/compilation/read_compilation_cfg.py index 7a9af801..45518701 100755 --- a/scripts/compilation/read_compilation_cfg.py +++ b/scripts/compilation/read_compilation_cfg.py @@ -1,8 +1,8 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- import os, sys -import ConfigParser +import configparser def get_l_option_section(config): @@ -17,10 +17,10 @@ def get_compilation_option(pwd_cfg, flag_name): Return the flag compilation of a compile.cfg located in pwd_cfg """ if not os.path.isfile(pwd_cfg): - print "Configuration file %s not found"%(pwd_cfg) + print("Configuration file %s not found"%(pwd_cfg)) sys.exit(1) - config = ConfigParser.ConfigParser() + config = configparser.ConfigParser(inline_comment_prefixes=(';','#')) config.read(pwd_cfg) if flag_name == "FC" and config.getboolean("OPTION","CACHE"): @@ -33,7 +33,7 @@ def get_compilation_option(pwd_cfg, flag_name): for section in ["COMMON"] + l_option_section: try: l.extend(config.get(section, flag_name).split()) - except ConfigParser.NoOptionError: + except configparser.NoOptionError: pass return " ".join(l) @@ -43,5 +43,5 @@ if __name__ == '__main__': qpackage_root = os.environ['QP_ROOT'] pwd_cfg = os.path.join(qpackage_root, "config/ifort_gpi2.cfg") - print get_compilation_option(pwd_cfg, "FC") - print get_compilation_option(pwd_cfg, "FCFLAGS") + print(get_compilation_option(pwd_cfg, "FC")) + print(get_compilation_option(pwd_cfg, "FCFLAGS")) diff --git a/scripts/ezfio_interface/ei_handler.py b/scripts/ezfio_interface/ei_handler.py index 23a0ce53..446d60d0 100755 --- a/scripts/ezfio_interface/ei_handler.py +++ b/scripts/ezfio_interface/ei_handler.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Welcome to the ei_handler. @@ -72,7 +72,7 @@ import sys import os import os.path -import ConfigParser +import configparser from collections import defaultdict from collections import namedtuple @@ -220,8 +220,8 @@ def get_dict_config_file(module_obj): # L o a d _ C o n f i g # # ~#~#~#~#~#~#~#~#~#~#~ # - config_file = ConfigParser.ConfigParser() - config_file.readfp(open(module_obj.path)) + config_file = configparser.ConfigParser() + config_file.read_file(open(module_obj.path)) # ~#~#~#~#~#~#~#~#~ # # F i l l _ d i c t # @@ -229,7 +229,7 @@ def get_dict_config_file(module_obj): def error(o, p, c): "o option ; p provider_name ;c module_obj.path" - print "You need a {0} for {1} in {2}".format(o, p, c) + print("You need a {0} for {1} in {2}".format(o, p, c)) for section in config_file.sections(): # pvd = provider @@ -245,13 +245,13 @@ def get_dict_config_file(module_obj): # Check if type is avalaible try: type_ = config_file.get(section, "type").strip() - except ConfigParser.NoOptionError: + except configparser.NoOptionError: error("type", pvd, module_obj.path) sys.exit(1) if type_ not in type_dict: - print "{0} not avalaible. Choose in:".format(type_).strip() - print ", ".join(sorted([i for i in type_dict])) + print("{0} not avalaible. Choose in:".format(type_).strip()) + print(", ".join(sorted([i for i in type_dict]))) sys.exit(1) else: d[pvd]["type"] = type_dict[type_] @@ -259,18 +259,18 @@ def get_dict_config_file(module_obj): # Fill the dict with REQUIRED information try: d[pvd]["doc"] = config_file.get(section, "doc") - except ConfigParser.NoOptionError: + except configparser.NoOptionError: error("doc", pvd, module_obj.path) sys.exit(1) try: interface = [i.lower().strip() for i in config_file.get(section, "interface").split(",")] - except ConfigParser.NoOptionError: + except configparser.NoOptionError: error("doc", pvd, module_obj.path) sys.exit(1) else: if not any(i in ["ezfio", "provider", "ocaml"] for i in interface): - print "Bad keyword for interface for {0}".format(pvd) + print("Bad keyword for interface for {0}".format(pvd)) sys.exit(1) else: d[pvd]["interface"] = interface @@ -279,7 +279,7 @@ def get_dict_config_file(module_obj): for option in l_info_optional: try: d[pvd][option] = config_file.get(section, option).lower() - except ConfigParser.NoOptionError: + except configparser.NoOptionError: if option in d_default: d[pvd][option] = d_default[option] @@ -287,7 +287,7 @@ def get_dict_config_file(module_obj): try: default_raw = config_file.get(section, "default") - except ConfigParser.NoOptionError: + except configparser.NoOptionError: if "ocaml" in d[pvd]["interface"]: error("default", pvd, module_obj.path) sys.exit(1) @@ -322,7 +322,7 @@ def create_ezfio_provider(dict_ezfio_cfg): dict_code_provider = dict() ez_p = EZFIO_Provider() - for provider_name, dict_info in dict_ezfio_cfg.iteritems(): + for provider_name, dict_info in dict_ezfio_cfg.items(): if "provider" in dict_info["interface"]: ez_p.set_type(dict_info['type'].fortran) ez_p.set_name(provider_name) @@ -364,7 +364,7 @@ def save_ezfio_provider(path_head, dict_code_provider): "! from file {0}/EZFIO.cfg".format(path_head), "\n"] - l_output += [code for code in dict_code_provider.values()] + l_output += [code for code in list(dict_code_provider.values())] output = "\n".join(l_output) @@ -381,22 +381,22 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"): def size_format_to_ezfio(size_raw): """ If size_raw == "=" is a formula -> do nothing; return - Else convert the born of a multidimential array + Else convert the range of a multidimential array (12,begin:end) into (12,begin+end+1) for example - If the value are between parenthses -> do nothing; return + If the values are between parenthses -> do nothing; return """ size_raw = str(size_raw) if size_raw.startswith('='): size_convert = size_raw.replace('.', '_') else: - size_raw = provider_info["size"].translate(None, "()") + size_raw = provider_info["size"].translate(str.maketrans("","","()")) size_raw = size_raw.replace('.', '_') a_size_raw = [] for dim in size_raw.split(","): try: - (begin, end) = map(str.strip, dim.split(":")) + (begin, end) = list(map(str.strip, dim.split(":"))) except ValueError: a_size_raw.append(dim) else: @@ -423,7 +423,7 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"): lenmax_name = max([len(i) for i in dict_ezfio_cfg]) lenmax_type = max([len(i["type"].fortran) - for i in dict_ezfio_cfg.values()]) + for i in list(dict_ezfio_cfg.values())]) str_name_format = create_format_string(lenmax_name + 2) str_type_format = create_format_string(lenmax_type + 2) @@ -433,15 +433,15 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"): # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# # # Checking is many ezfio_dir provided - l_ezfio_dir = [d['ezfio_dir'] for d in dict_ezfio_cfg.values()] + l_ezfio_dir = [d['ezfio_dir'] for d in list(dict_ezfio_cfg.values())] if not l_ezfio_dir.count(l_ezfio_dir[0]) == len(l_ezfio_dir): - print >> sys.stderr, "You have many ezfio_dir. Not supported yet" + print("You have many ezfio_dir. Not supported yet", file=sys.stderr) raise TypeError else: result = [l_ezfio_dir[0]] - for provider_name, provider_info in sorted(dict_ezfio_cfg.iteritems()): + for provider_name, provider_info in sorted(dict_ezfio_cfg.items()): # Get the value from dict name_raw = provider_info["ezfio_name"].lower() @@ -532,7 +532,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower): l_type = [] l_doc = [] - for k, v in dict_ezfio_cfg.iteritems(): + for k, v in dict_ezfio_cfg.items(): if "ocaml" in v['interface']: l_ezfio_name.append(v['ezfio_name']) l_type.append(v["type"]) @@ -580,7 +580,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower): '(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)', ""] - for provider_name, d_val in sorted(dict_ezfio_cfg.iteritems()): + for provider_name, d_val in sorted(dict_ezfio_cfg.items()): if 'default' not in d_val: continue @@ -655,7 +655,7 @@ def get_l_module_with_auto_generate_ocaml_lower(): l_module_lower = [] import re - p = re.compile(ur'interface:.*ocaml') + p = re.compile(r'interface:.*ocaml') for f in l_folder: path = "{0}/{1}/EZFIO.cfg".format(QP_SRC, f) @@ -782,7 +782,7 @@ if __name__ == "__main__": # if arguments["list_supported_types"]: for i in sorted(get_type_dict()): - print i + print(i) sys.exit(0) if arguments["ocaml_global"]: diff --git a/scripts/ezfio_interface/ezfio_generate_ocaml.py b/scripts/ezfio_interface/ezfio_generate_ocaml.py index 3c905122..191470d8 100755 --- a/scripts/ezfio_interface/ezfio_generate_ocaml.py +++ b/scripts/ezfio_interface/ezfio_generate_ocaml.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ This program generates all the OCaml templates needed by qp_edit @@ -17,12 +17,12 @@ class EZFIO_ocaml(object): def __init__(self, **kwargs): - for k, v in kwargs.iteritems(): + for k, v in kwargs.items(): try: - exec "self.{0} = {1}".format(k, v) + exec("self.{0} = {1}".format(k, v)) except NameError: - exec "self.{0} = '{1}'".format(k, v) + exec("self.{0} = '{1}'".format(k, v)) @property def Ocaml_type(self): @@ -39,7 +39,7 @@ class EZFIO_ocaml(object): def check_if_init(self, l_arg, name): for i in l_arg: try: - exec "self.{0}".format(i) + exec("self.{0}".format(i)) except AttributeError: msg = "You need to provide a '{0}' for creating {1}" raise KeyError(msg.format(i, name)) diff --git a/scripts/ezfio_interface/ezfio_generate_provider.py b/scripts/ezfio_interface/ezfio_generate_provider.py index 46df7e5e..4b43a88a 100755 --- a/scripts/ezfio_interface/ezfio_generate_provider.py +++ b/scripts/ezfio_interface/ezfio_generate_provider.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 __author__ = "Applencourt PEP8" __date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)" @@ -88,7 +88,7 @@ END_PROVIDER def __init__(self): self.values = "type doc name ezfio_dir ezfio_name write output".split() for v in self.values: - exec "self.{0} = None".format(v) + exec("self.{0} = None".format(v)) def __repr__(self): self.set_write() @@ -96,7 +96,7 @@ END_PROVIDER for v in self.values: if not v: msg = "Error : %s is not set in EZFIO.cfg" % (v) - print >>sys.stderr, msg + print(msg, file=sys.stderr) sys.exit(1) if "size" not in self.__dict__: self.__dict__["size"] = "" @@ -167,7 +167,7 @@ def test_module(): T.set_ezfio_dir("Hartree_Fock") T.set_ezfio_name("thresh_SCF") T.set_output("output_Hartree_Fock") - print T + print(T) if __name__ == '__main__': test_module() diff --git a/scripts/generate_h_apply.py b/scripts/generate_h_apply.py index 8c399e55..dc7d340e 100644 --- a/scripts/generate_h_apply.py +++ b/scripts/generate_h_apply.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 import os @@ -11,6 +11,7 @@ declarations decls_main deinit_thread init_main +filter_integrals filter2p filter2h2p_double filter2h2p_single @@ -104,6 +105,11 @@ class H_apply(object): s["do_mono_excitations"] = d[do_mono_exc] s["do_double_excitations"] = d[do_double_exc] s["keys_work"] += "call fill_H_apply_buffer_no_selection(key_idx,keys_out,N_int,iproc)" + s["filter_integrals"] = "array_pairs = .True." + if SingleRef: + s["filter_integrals"] = """ + call get_mo_bielec_integrals_existing_ik(i_a,j_a,mo_num,array_pairs,mo_integrals_map) + """ s["generate_psi_guess"] = """ ! Sort H_jj to find the N_states lowest states @@ -149,7 +155,7 @@ class H_apply(object): def __repr__(self): buffer = self.template - for key,value in self.data.items(): + for key,value in list(self.data.items()): buffer = buffer.replace('$'+key, value) return buffer diff --git a/scripts/hello.py b/scripts/hello.py index c533a0f4..a575026e 100644 --- a/scripts/hello.py +++ b/scripts/hello.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 import random @@ -131,8 +131,8 @@ _ __ `/___ __ \__ ___/__ __ \ """ ] - print random.choice(hello) - print "\n -- Quantum Package Shell --\n" + print(random.choice(hello)) + print("\n -- Quantum Package Shell --\n") diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index 160a1ce9..a6bb6d3f 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Module utilitary @@ -25,7 +25,7 @@ try: from docopt import docopt from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO except ImportError: - print "source .quantum_package.rc" + print("source .quantum_package.rc") raise @@ -50,6 +50,7 @@ def get_binaries(path_module): stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = process.communicate() + stdout = stdout.decode() except OSError: return [] else: @@ -106,9 +107,9 @@ def get_l_module_descendant(d_child, l_module): try: l.extend(get_l_module_descendant(d_child, d_child[module])) except KeyError: - print >> sys.stderr, "Error: " - print >> sys.stderr, "`{0}` is not a submodule".format(module) - print >> sys.stderr, "Check the typo (spelling, case, '/', etc.) " + print("Error: ", file=sys.stderr) + print("`{0}` is not a submodule".format(module), file=sys.stderr) + print("Check the typo (spelling, case, '/', etc.) ", file=sys.stderr) sys.exit(1) return list(set(l)) @@ -120,7 +121,7 @@ class ModuleHandler(): @property def l_module(self): - return self.dict_child.keys() + return list(self.dict_child.keys()) @property def dict_parent(self): @@ -132,7 +133,7 @@ class ModuleHandler(): d = {} for module_name in d_child: - d[module_name] = [i for i in d_child.keys() + d[module_name] = [i for i in list(d_child.keys()) if module_name in d_child[i]] return d @@ -151,8 +152,8 @@ class ModuleHandler(): d[module_name] = get_l_module_descendant(d_child, d_child[module_name]) except KeyError: - print "Check NEED for {0}".format( - module_name) + print("Check NEED for {0}".format( + module_name)) sys.exit(1) return d @@ -185,7 +186,7 @@ class ModuleHandler(): for e in d_desc[module]: d[e] = 1 - return d.keys() + return list(d.keys()) def l_reduce_tree(self, l_module): """For a list of module in input return only the root""" @@ -218,8 +219,8 @@ if __name__ == '__main__': for module in l_module: if not is_module(module): - print "{0} is not a valid module. Abort".format(module) - print "No NEED in it" + print("{0} is not a valid module. Abort".format(module)) + print("No NEED in it") sys.exit(1) m = ModuleHandler() @@ -227,7 +228,7 @@ if __name__ == '__main__': if arguments['print_descendant']: for module in l_module: - print " ".join(sorted(m.l_descendant_unique([module]))) + print(" ".join(sorted(m.l_descendant_unique([module])))) if arguments["clean"]: diff --git a/scripts/perturbation.py b/scripts/perturbation.py index cefb89b2..0fe6cfc8 100644 --- a/scripts/perturbation.py +++ b/scripts/perturbation.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 import os from qp_path import QP_SRC @@ -7,7 +7,7 @@ Pert_dir = os.path.join(QP_SRC,"perturbation") perturbations = [] -for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)): +for filename in [x for x in os.listdir(Pert_dir) if x.endswith(".irp.f")]: filename = os.path.join(Pert_dir,filename) file = open(filename,'r') @@ -22,6 +22,6 @@ for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)): if __name__ == '__main__': - print 'Perturbations:' + print('Perturbations:') for k in perturbations: - print '* ', k + print('* ', k) diff --git a/scripts/utility/get_groups b/scripts/utility/get_groups index 0d79cae2..418ea6ec 100755 --- a/scripts/utility/get_groups +++ b/scripts/utility/get_groups @@ -1,7 +1,7 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- -import urllib +import urllib.request, urllib.parse, urllib.error import sys from bs4 import BeautifulSoup @@ -35,11 +35,11 @@ def clean_up(text): return False else: return y[0] in irred - data = filter(f,data)[:len(irred)] + data = list(filter(f,data))[:len(irred)] for line in data: s = line.replace('*','').split() l = irred[s[0]] - data[l] = map(float,s[1:len(irred)+1]) + data[l] = list(map(float,s[1:len(irred)+1])) d = {} e = {} @@ -48,23 +48,23 @@ def clean_up(text): for k in sop: e[sop[k]] = k n = len(irred) - print "Group\t", group, "\nn\t", n - print "\n \tIrred \tOperation" + print("Group\t", group, "\nn\t", n) + print("\n \tIrred \tOperation") for i in range(n): - print "%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)) + print("%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10))) - print "\nTable\n ", + print("\nTable\n ", end=' ') for j in range(n): - print "%8s "%(str(j+1).center(8)), + print("%8s "%(str(j+1).center(8)), end=' ') for i in range(n): - print "\n%4d "%(i+1), + print("\n%4d "%(i+1), end=' ') for j in range(n): - print "%8.5f "%(data[i][j]), - print "\n" + print("%8.5f "%(data[i][j]), end=' ') + print("\n") def main(): for group in sys.argv[1:]: - f = urllib.urlopen(address%(group)) + f = urllib.request.urlopen(address%(group)) html = f.read().split('\n',1)[1] text = clean_up(html) diff --git a/scripts/utility/qp_bitmasks.py b/scripts/utility/qp_bitmasks.py index 5107576b..38aa48d7 100644 --- a/scripts/utility/qp_bitmasks.py +++ b/scripts/utility/qp_bitmasks.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 BIT_KIND_SIZE=64 diff --git a/scripts/utility/qp_path.py b/scripts/utility/qp_path.py index 0844c06f..11756920 100644 --- a/scripts/utility/qp_path.py +++ b/scripts/utility/qp_path.py @@ -1,13 +1,14 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- + import os import sys try: QP_ROOT = os.environ['QP_ROOT'] except: - print "source quantum_package.rc" + print("source quantum_package.rc") sys.exit(1) else: QP_EZFIO = os.environ["QP_EZFIO"] diff --git a/src/cipsi/cipsi.irp.f b/src/cipsi/cipsi.irp.f index ba922c49..a6ab6f8e 100644 --- a/src/cipsi/cipsi.irp.f +++ b/src/cipsi/cipsi.irp.f @@ -108,6 +108,7 @@ subroutine run_cipsi n_det_before = N_det to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor) to_select = max(N_states_diag, to_select) + to_select = max(to_select,1) call ZMQ_selection(to_select, pt2, variance, norm) PROVIDE psi_coef diff --git a/src/cipsi/energy.irp.f b/src/cipsi/energy.irp.f index 0ae5ad79..37b29593 100644 --- a/src/cipsi/energy.irp.f +++ b/src/cipsi/energy.irp.f @@ -22,8 +22,6 @@ BEGIN_PROVIDER [ double precision, pt2_E0_denominator, (N_states) ] enddo else if (h0_type == "Barycentric") then pt2_E0_denominator(1:N_states) = barycentric_electronic_energy(1:N_states) - else if (h0_type == "Variance") then - pt2_E0_denominator(1:N_states) = psi_energy(1:N_states) !1.d0-nuclear_repulsion else if (h0_type == "SOP") then pt2_E0_denominator(1:N_states) = psi_energy(1:N_states) else diff --git a/src/cis/20.cis.bats b/src/cis/20.cis.bats index 130924d2..6dcb2c52 100644 --- a/src/cis/20.cis.bats +++ b/src/cis/20.cis.bats @@ -64,7 +64,7 @@ function run() { @test "SO" { # 1.9667s 2.91234s [[ -n $TRAVIS ]] && skip - run so.ezfio -25.7502102903664 -25.586265109319484 -25.582920204099572 + run so.ezfio -25.750224071640112 -25.586278842164113 -25.582933929660470 } @test "OH" { # 2.201s 2.65573s diff --git a/src/cis/h_apply.irp.f b/src/cis/h_apply.irp.f index 95aa52e4..14389bed 100644 --- a/src/cis/h_apply.irp.f +++ b/src/cis/h_apply.irp.f @@ -1,14 +1,14 @@ ! Generates subroutine H_apply_cis ! -------------------------------- -BEGIN_SHELL [ /usr/bin/env python2 ] +BEGIN_SHELL [ /usr/bin/env python3 ] from generate_h_apply import H_apply H = H_apply("cis",do_double_exc=False) -print H +print(H) H = H_apply("cis_sym",do_double_exc=False) H.filter_only_connected_to_hf() -print H +print(H) END_SHELL diff --git a/src/cisd/h_apply.irp.f b/src/cisd/h_apply.irp.f index b18f6373..fa647f8a 100644 --- a/src/cisd/h_apply.irp.f +++ b/src/cisd/h_apply.irp.f @@ -1,13 +1,13 @@ ! Generates subroutine H_apply_cisd ! ---------------------------------- -BEGIN_SHELL [ /usr/bin/env python2 ] +BEGIN_SHELL [ /usr/bin/env python3 ] from generate_h_apply import H_apply H = H_apply("cisd",do_double_exc=True) -print H +print(H) H = H_apply("cisd_sym",do_double_exc=True) H.filter_only_connected_to_hf() -print H +print(H) END_SHELL diff --git a/src/davidson/diagonalize_ci.irp.f b/src/davidson/diagonalize_ci.irp.f index 8339406f..996011cd 100644 --- a/src/davidson/diagonalize_ci.irp.f +++ b/src/davidson/diagonalize_ci.irp.f @@ -118,22 +118,22 @@ END_PROVIDER call u_0_S2_u_0(s2_eigvalues,eigenvectors,N_det,psi_det,N_int,& N_det,size(eigenvectors,1)) if (only_expected_s2) then - do j=1,N_det - ! Select at least n_states states with S^2 values closed to "expected_s2" - if(dabs(s2_eigvalues(j)-expected_s2).le.0.5d0)then - i_state +=1 - index_good_state_array(i_state) = j - good_state_array(j) = .True. - endif - if(i_state.eq.N_states) then - exit - endif - enddo - else - do j=1,N_det - index_good_state_array(j) = j + do j=1,N_det + ! Select at least n_states states with S^2 values closed to "expected_s2" + if(dabs(s2_eigvalues(j)-expected_s2).le.0.5d0)then + i_state +=1 + index_good_state_array(i_state) = j good_state_array(j) = .True. - enddo + endif + if(i_state.eq.N_states) then + exit + endif + enddo + else + do j=1,N_det + index_good_state_array(j) = j + good_state_array(j) = .True. + enddo endif if(i_state .ne.0)then ! Fill the first "i_state" states that have a correct S^2 value @@ -163,7 +163,7 @@ END_PROVIDER print*,'!!!!!!!! WARNING !!!!!!!!!' print*,' Within the ',N_det,'determinants selected' print*,' and the ',N_states_diag,'states requested' - print*,' We did not find any state with S^2 values close to ',expected_s2 + print*,' We did not find only states with S^2 values close to ',expected_s2 print*,' We will then set the first N_states eigenvectors of the H matrix' print*,' as the CI_eigenvectors' print*,' You should consider more states and maybe ask for s2_eig to be .True. or just enlarge the CI space' @@ -179,11 +179,11 @@ END_PROVIDER deallocate(index_good_state_array,good_state_array) deallocate(s2_eigvalues) else - call lapack_diag(eigenvalues,eigenvectors, & + call lapack_diag(eigenvalues,eigenvectors, & H_matrix_all_dets,size(H_matrix_all_dets,1),N_det) CI_electronic_energy(:) = 0.d0 - call u_0_S2_u_0(CI_s2,eigenvectors,N_det,psi_det,N_int,& - min(N_det,N_states_diag),size(eigenvectors,1)) + call u_0_S2_u_0(CI_s2,eigenvectors,N_det,psi_det,N_int, & + min(N_det,N_states_diag),size(eigenvectors,1)) ! Select the "N_states_diag" states of lowest energy do j=1,min(N_det,N_states_diag) do i=1,N_det @@ -213,7 +213,7 @@ subroutine diagonalize_CI ! Replace the coefficients of the |CI| states by the coefficients of the ! eigenstates of the |CI| matrix. END_DOC - integer :: i,j + integer :: i,j do j=1,N_states do i=1,N_det psi_coef(i,j) = CI_eigenvectors(i,j) diff --git a/src/density_for_dft/EZFIO.cfg b/src/density_for_dft/EZFIO.cfg index 86bbaeb1..42b8eab4 100644 --- a/src/density_for_dft/EZFIO.cfg +++ b/src/density_for_dft/EZFIO.cfg @@ -1,25 +1,23 @@ [density_for_dft] type: character*(32) -doc: Type of density used for DFT calculation. If set to WFT , it uses the density of the wave function stored in (psi_det,psi_coef). If set to input_density it uses the one-body dm stored in aux_quantities/ . If set to damping_rs_dft it uses the damped density between WFT and input_density. In the ks_scf and rs_ks_scf programs, it is set to WFT. +doc: Type of density used for DFT calculation. If set to WFT , it uses the density of the wave function stored in (psi_det,psi_coef). If set to input_density it uses the one-body dm stored in aux_quantities/ . If set to damping_rs_dft it uses the damped density between WFT and input_density. In the ks_scf and rs_ks_scf programs, it is set to WFT. interface: ezfio, provider, ocaml -default: WFT +default: WFT [damping_for_rs_dft] type: double precision -doc: damping factor for the density used in RSFT. +doc: damping factor for the density used in RSFT. interface: ezfio,provider,ocaml default: 0.5 [no_core_density] type: character*(32) -doc: Type of density -doc: if [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero +doc: Type of density. If [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero interface: ezfio, provider, ocaml default: full_density [normalize_dm] type: logical -doc: Type of density -doc: if .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb +doc: Type of density. If .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb interface: ezfio, provider, ocaml default: True diff --git a/src/determinants/EZFIO.cfg b/src/determinants/EZFIO.cfg index 40897159..ef00080b 100644 --- a/src/determinants/EZFIO.cfg +++ b/src/determinants/EZFIO.cfg @@ -76,7 +76,6 @@ type: integer interface: ezfio doc: Number of determinants to print in qp_edit type: integer -interface: ezfio [psi_coef] interface: ezfio diff --git a/src/determinants/h_apply.template.f b/src/determinants/h_apply.template.f index f16d2e7f..abdd6862 100644 --- a/src/determinants/h_apply.template.f +++ b/src/determinants/h_apply.template.f @@ -243,7 +243,7 @@ subroutine $subroutine_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl ! Build array of the non-zero integrals of second excitation $filter_integrals - if (ispin == 1) then + if (ispin == 1) then integer :: jjj i=0 @@ -285,7 +285,7 @@ subroutine $subroutine_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl $only_1h_double $only_1p_double $only_2h1p_double - $filter_only_connected_to_hf_double + $filter_only_connected_to_hf_double key_idx += 1 do k=1,N_int keys_out(k,1,key_idx) = key(k,1) @@ -497,7 +497,7 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generato $filter_only_1h1p_single $filter_only_1h2p_single $filter_only_2h2p_single - $filter_only_connected_to_hf_single + $filter_only_connected_to_hf_single key_idx += 1 do k=1,N_int keys_out(k,1,key_idx) = hole(k,1) diff --git a/src/dft_one_e/e_xc_general.irp.f b/src/dft_one_e/e_xc_general.irp.f index fc9f9fd2..6c9e7bd3 100644 --- a/src/dft_one_e/e_xc_general.irp.f +++ b/src/dft_one_e/e_xc_general.irp.f @@ -3,8 +3,8 @@ BEGIN_PROVIDER [double precision, energy_x, (N_states)] BEGIN_DOC ! correlation energies general providers. END_DOC - - BEGIN_SHELL [ /usr/bin/env python2 ] + + BEGIN_SHELL [ /usr/bin/env python3 ] import os import glob from qp_path import QP_SRC @@ -13,32 +13,32 @@ os.chdir(funcdir) functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) prefix = "" for f in functionals: - print """ + print(""" %sif (trim(exchange_functional) == '%s') then - energy_x = (1.d0 - HF_exchange ) * energy_x_%s"""%(prefix, f, f) + energy_x = (1.d0 - HF_exchange ) * energy_x_%s"""%(prefix, f, f)) prefix = "else " -print """ +print(""" else print *, 'exchange functional required does not exist ...' print *, 'exchange_functional ',exchange_functional - stop""" -print "endif" + stop""") +print("endif") END_SHELL - - + + END_PROVIDER - - - - + + + + BEGIN_PROVIDER [double precision, energy_c, (N_states)] implicit none BEGIN_DOC ! correlation and exchange energies general providers. END_DOC - - BEGIN_SHELL [ /usr/bin/env python2 ] + + BEGIN_SHELL [ /usr/bin/env python3 ] import os import glob from qp_path import QP_SRC @@ -47,19 +47,19 @@ os.chdir(funcdir) functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) prefix = "" for f in functionals: - print """ + print(""" %sif (trim(correlation_functional) == '%s') then - energy_c = energy_c_%s"""%(prefix, f, f) + energy_c = energy_c_%s"""%(prefix, f, f) ) prefix = "else " -print """ +print(""" else print*, 'Correlation functional required does not exist ...' print*,'correlation_functional ',correlation_functional - stop""" -print "endif" + stop""") +print("endif") END_SHELL - + END_PROVIDER diff --git a/src/dft_one_e/pot_general.irp.f b/src/dft_one_e/pot_general.irp.f index 2f45a464..df292422 100644 --- a/src/dft_one_e/pot_general.irp.f +++ b/src/dft_one_e/pot_general.irp.f @@ -4,8 +4,8 @@ BEGIN_DOC ! general providers for the alpha/beta exchange potentials on the AO basis END_DOC - - BEGIN_SHELL [ /usr/bin/env python2 ] + + BEGIN_SHELL [ /usr/bin/env python3 ] import os import glob from qp_path import QP_SRC @@ -15,33 +15,33 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) prefix = "" for f in functionals: - print """ + print(""" %sif (trim(exchange_functional) == '%s') then potential_x_alpha_ao = ( 1.d0 - HF_exchange ) * potential_x_alpha_ao_%s - potential_x_beta_ao = ( 1.d0 - HF_exchange ) * potential_x_beta_ao_%s"""%(prefix, f, f, f) + potential_x_beta_ao = ( 1.d0 - HF_exchange ) * potential_x_beta_ao_%s"""%(prefix, f, f, f) ) prefix = "else " -print """ +print(""" else print*, 'exchange functional required does not exist ...' print*,'exchange_functional ',exchange_functional - stop""" -print "endif" + stop""") +print("endif") END_SHELL - - + + END_PROVIDER - - - + + + BEGIN_PROVIDER [double precision, potential_c_alpha_ao,(ao_num,ao_num,N_states)] &BEGIN_PROVIDER [double precision, potential_c_beta_ao,(ao_num,ao_num,N_states)] implicit none BEGIN_DOC ! general providers for the alpha/beta correlation potentials on the AO basis END_DOC - - BEGIN_SHELL [ /usr/bin/env python2 ] + + BEGIN_SHELL [ /usr/bin/env python3 ] import os import glob from qp_path import QP_SRC @@ -51,27 +51,27 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) prefix = "" for f in functionals: - print """ + print(""" %sif (trim(correlation_functional) == '%s') then potential_c_alpha_ao = potential_c_alpha_ao_%s - potential_c_beta_ao = potential_c_beta_ao_%s"""%(prefix, f, f, f) + potential_c_beta_ao = potential_c_beta_ao_%s"""%(prefix, f, f, f) ) prefix = "else " -print """ +print(""" else print*, 'Correlation functional required does not exist ...' print*,'correlation_functional ',correlation_functional - stop""" -print "endif" + stop""" ) +print("endif") END_SHELL - + END_PROVIDER - - - - - + + + + + BEGIN_PROVIDER [double precision, potential_x_alpha_mo,(mo_num,mo_num,N_states)] &BEGIN_PROVIDER [double precision, potential_x_beta_mo ,(mo_num,mo_num,N_states)] implicit none @@ -86,7 +86,7 @@ print "endif" potential_x_alpha_mo(1,1,istate), & size(potential_x_alpha_mo,1) & ) - + call ao_to_mo( & potential_x_beta_ao(1,1,istate), & size(potential_x_beta_ao,1), & @@ -94,9 +94,9 @@ print "endif" size(potential_x_beta_mo,1) & ) enddo - + END_PROVIDER - + BEGIN_PROVIDER [double precision, potential_c_alpha_mo,(mo_num,mo_num,N_states)] &BEGIN_PROVIDER [double precision, potential_c_beta_mo, (mo_num,mo_num,N_states)] implicit none @@ -111,7 +111,7 @@ print "endif" potential_c_alpha_mo(1,1,istate), & size(potential_c_alpha_mo,1) & ) - + call ao_to_mo( & potential_c_beta_ao(1,1,istate), & size(potential_c_beta_ao,1), & @@ -119,7 +119,7 @@ print "endif" size(potential_c_beta_mo,1) & ) enddo - + END_PROVIDER @@ -147,9 +147,9 @@ print "endif" enddo Trace_v_Hxc(istate) = Trace_v_xc(istate) + Trace_v_H(istate) enddo - + END_PROVIDER - + BEGIN_PROVIDER [double precision, Trace_v_xc_new, (N_states)] implicit none integer :: i,j,istate @@ -166,14 +166,14 @@ print "endif" enddo enddo enddo - + END_PROVIDER - + BEGIN_PROVIDER [double precision, potential_xc_alpha_mo,(mo_num,mo_num,N_states)] &BEGIN_PROVIDER [double precision, potential_xc_beta_mo,(mo_num,mo_num,N_states)] implicit none integer :: istate - + do istate = 1, N_states call ao_to_mo( & potential_xc_alpha_ao(1,1,istate), & @@ -181,7 +181,7 @@ print "endif" potential_xc_alpha_mo(1,1,istate), & size(potential_xc_alpha_mo,1) & ) - + call ao_to_mo( & potential_xc_beta_ao(1,1,istate), & size(potential_xc_beta_ao,1), & @@ -189,18 +189,18 @@ print "endif" size(potential_xc_beta_mo,1) & ) enddo - + END_PROVIDER - - + + BEGIN_PROVIDER [double precision, potential_xc_alpha_ao,(ao_num,ao_num,N_states)] &BEGIN_PROVIDER [double precision, potential_xc_beta_ao,(ao_num,ao_num,N_states)] implicit none BEGIN_DOC ! general providers for the alpha/beta exchange/correlation potentials on the AO basis END_DOC - - BEGIN_SHELL [ /usr/bin/env python2 ] + + BEGIN_SHELL [ /usr/bin/env python3 ] import os import glob from qp_path import QP_SRC @@ -210,19 +210,19 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) prefix = "" for f in functionals: - print """ + print(""" %sif (trim(exchange_functional) == '%s') then potential_xc_alpha_ao = potential_xc_alpha_ao_%s - potential_xc_beta_ao = potential_xc_beta_ao_%s"""%(prefix, f, f, f) + potential_xc_beta_ao = potential_xc_beta_ao_%s"""%(prefix, f, f, f) ) prefix = "else " -print """ +print(""" else print*, 'exchange functional required does not exist ...' print*,'exchange_functional ',exchange_functional - stop""" -print "endif" + stop""") +print("endif") END_SHELL - + END_PROVIDER diff --git a/src/perturbation/perturbation.irp.f b/src/perturbation/perturbation.irp.f index 040f3026..cde52027 100644 --- a/src/perturbation/perturbation.irp.f +++ b/src/perturbation/perturbation.irp.f @@ -1,4 +1,4 @@ -BEGIN_SHELL [ /usr/bin/env python2 ] +BEGIN_SHELL [ /usr/bin/env python3 ] from perturbation import perturbations import os @@ -8,6 +8,6 @@ template = file.read() file.close() for p in perturbations: - print template.replace("$PERT",p) + print(template.replace("$PERT",p)) END_SHELL diff --git a/src/perturbation/perturbation.template.f b/src/perturbation/perturbation.template.f index 0a7ca181..558b92a9 100644 --- a/src/perturbation/perturbation.template.f +++ b/src/perturbation/perturbation.template.f @@ -1,4 +1,4 @@ -BEGIN_SHELL [ /usr/bin/env python2 ] +BEGIN_SHELL [ /usr/bin/env python3 ] import perturbation END_SHELL diff --git a/src/scf_utils/diagonalize_fock.irp.f b/src/scf_utils/diagonalize_fock.irp.f index 865b4d31..d501278f 100644 --- a/src/scf_utils/diagonalize_fock.irp.f +++ b/src/scf_utils/diagonalize_fock.irp.f @@ -7,11 +7,11 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) integer :: i,j integer :: liwork, lwork, n, info integer, allocatable :: iwork(:) - double precision, allocatable :: work(:), F(:,:), S(:,:) + double precision, allocatable :: work(:), F(:,:), F_save(:,:) double precision, allocatable :: diag(:) - allocate( F(mo_num,mo_num) ) + allocate( F(mo_num,mo_num), F_save(mo_num,mo_num) ) allocate (diag(mo_num) ) do j=1,mo_num @@ -51,6 +51,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) lwork = -1 liwork = -1 + F_save = F call dsyevd( 'V', 'U', mo_num, F, & size(F,1), diag, work, lwork, iwork, liwork, info) @@ -71,6 +72,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) if (info /= 0) then + F = F_save call dsyev( 'V', 'L', mo_num, F, & size(F,1), diag, work, lwork, info) @@ -83,7 +85,7 @@ BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) call dgemm('N','N',ao_num,mo_num,mo_num, 1.d0, & mo_coef, size(mo_coef,1), F, size(F,1), & 0.d0, eigenvectors_Fock_matrix_mo, size(eigenvectors_Fock_matrix_mo,1)) - deallocate(work, F, diag) + deallocate(work, F, F_save, diag) END_PROVIDER diff --git a/src/scf_utils/roothaan_hall_scf.irp.f b/src/scf_utils/roothaan_hall_scf.irp.f index faf23a51..ea472cdf 100644 --- a/src/scf_utils/roothaan_hall_scf.irp.f +++ b/src/scf_utils/roothaan_hall_scf.irp.f @@ -299,6 +299,7 @@ END_DOC Fock_matrix_AO_(i,j) = 0.d0 enddo do k=1,dim_DIIS + if (dabs(X_vector_DIIS(k)) < 1.d-10) cycle do i=1,ao_num Fock_matrix_AO_(i,j) = Fock_matrix_AO_(i,j) + & X_vector_DIIS(k)*Fock_matrix_DIIS(i,j,dim_DIIS-k+1) diff --git a/src/zmq/f77_zmq.h b/src/zmq/f77_zmq_free.h similarity index 100% rename from src/zmq/f77_zmq.h rename to src/zmq/f77_zmq_free.h diff --git a/src/zmq/f77_zmq_module.f90 b/src/zmq/f77_zmq_module.f90 index d0f551fa..1e4a5af3 100644 --- a/src/zmq/f77_zmq_module.f90 +++ b/src/zmq/f77_zmq_module.f90 @@ -1,4 +1,4 @@ module f77_zmq - include 'f77_zmq.h' + include 'f77_zmq_free.h' end module diff --git a/tests/bats_to_sh.py b/tests/bats_to_sh.py index 89bf1eb5..7194af77 100755 --- a/tests/bats_to_sh.py +++ b/tests/bats_to_sh.py @@ -1,11 +1,11 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 import sys with open(sys.argv[1],'r') as f: raw_data = f.read() -print "set -x" +print("set -x") output = [] inside = False @@ -25,9 +25,9 @@ for i in raw_data: level -= 1 output.append(new_i) -print "".join(output).replace("@test ", +print("".join(output).replace("@test ", """[[ -z $BATS_TEST_NUMBER ]] && BATS_TEST_NUMBER=0 || ((++BATS_TEST_NUMBER)) ; -export BATS_TEST_DESCRIPTION=""").replace("skip","return") +export BATS_TEST_DESCRIPTION=""").replace("skip","return"))