bug fixes

IO_kernel/Makefile

@@ -18,7 +18,6 @@ IFLAGS=
 
 IO_KERNEL_OBJS = \
 mpiio.o \
-my_mkdir.o \
 cubefile.o \
 function3d.o \
 pdep_io.o \

IO_kernel/function3d.f90

@@ -99,7 +99,7 @@ MODULE function3d
       IERR = kwargs%setitem("grid_function",charbase64)
       IERR = kwargs%setitem("dtype","double")
       !
-      IERR = call_py_noret(pymod, "base64_to_function3d", args, kwargs)
+      IERR = call_py_noret(pymod, "base64_to_function3D", args, kwargs)
       !
       CALL kwargs%destroy
       CALL args%destroy
@@ -162,7 +162,7 @@ MODULE function3d
       IERR = args%setitem(0, TRIM(ADJUSTL(fname)) )
       IERR = dict_create(kwargs)
       !
-      IERR = call_py(return_obj,pymod, "function3d_to_base64", args, kwargs)
+      IERR = call_py(return_obj,pymod, "function3D_to_base64", args, kwargs)
       !
       IERR = cast(return_dict, return_obj)
       !

Modules/westcom.f90

@@ -86,7 +86,7 @@ MODULE westin
   CHARACTER(LEN=512) :: qe_prefix
   CHARACTER(LEN=512) :: savedir            ! outdir/west_prefix.code.save
   CHARACTER(LEN=512) :: main_input_file    ! input file
-  CHARACTER(LEN=:), ALLOCATABLE :: logfile ! savedir/logfile.xml 
+  CHARACTER(LEN=512) :: logfile ! savedir/logfile.json 
   !
 END MODULE  
 !
@@ -148,8 +148,8 @@ MODULE wfreq_center
   INTEGER :: n_secant_maxiter
   REAL(DP) :: trev_secant
   LOGICAL :: l_enable_lanczos
-  CHARACTER(LEN=1) :: macropol_calculation
   LOGICAL :: l_enable_gwetot
+  CHARACTER(LEN=1) :: macropol_calculation
   REAL(DP) :: exx_etot
   REAL(DP) :: o_restart_time
   REAL(DP) :: ecut_spectralf(2)

Pytools/lockfile.py → Pytools/clientserver.py

@@ -67,6 +67,7 @@ class QboxServer(ClientServer) :
        #
        client_image = self.client_lockfile.split(".")[1] 
        self.server_inputfile = f"qb.{client_image}.in" # we assume that server_number = client_image
+       print(self.server_inputfile)
        #
        # List of perturbation files 
        #
@@ -102,7 +103,7 @@ class QboxServer(ClientServer) :
 # INTERFACE #
 #############
 
-def sleep_and_wait_for_lock_to_be_removed(*args, **kwargs):
+def sleep_and_wait(*args, **kwargs):
     #
     client_lockfile = args[0] # name of client lockfile 
     maxsec = 12 * 60 * 60 # 12 hours, Max sleep time (in s) 
@@ -127,7 +128,7 @@ def sleep_and_wait_for_lock_to_be_removed(*args, **kwargs):
 def test() :
     with open("I.1.lock","w") as f :
        f.write(" ")
-    sleep_and_wait_for_lock_to_be_removed("I.1.lock",maxsec=60,sleepsec=2)
+    sleep_and_wait("I.1.lock",maxsec=60,sleepsec=2)
 
 if __name__ == "__main__":
     # execute only if run as a script

Pytools/fetch_input.py

@@ -37,28 +37,29 @@ default["wstat_control"]["qlist"] = [ 1 ] # dynamically set to the actual number
 default["wfreq_control"] = {}
 default["wfreq_control"]["wfreq_calculation"] = "XWGQ"
 default["wfreq_control"]["n_pdep_eigen_to_use"] = 1 # dynamically set to the number of electrons
-default["wfreq_control"]["qp_bandrange"] = [1,2]
+default["wfreq_control"]["qp_bandrange"] = [1, 2]
 default["wfreq_control"]["macropol_calculation"] = 'N'
 default["wfreq_control"]["n_lanczos"] = 30
 default["wfreq_control"]["n_imfreq"] = 128 
-default["wfreq_control"]["n_refreq"] = 272 # dynamically set so that ecut_refreq / n_refreq = 0.1 eV 
+default["wfreq_control"]["n_refreq"] = 272  
 default["wfreq_control"]["ecut_imfreq"] = 25. # dynamically set to ecutrho
-default["wfreq_control"]["ecut_refreq"] = 2. # dynamically set to contain eks + 0.5 Ry padding 
+default["wfreq_control"]["ecut_refreq"] = 2. 
 default["wfreq_control"]["wfreq_eta"] = 0.05 / rytoev
 default["wfreq_control"]["n_secant_maxiter"] = 21
 default["wfreq_control"]["trev_secant"] = 0.05 / rytoev
 default["wfreq_control"]["l_enable_lanczos"] = True
+default["wfreq_control"]["l_enable_gwetot"] = False
 default["wfreq_control"]["o_restart_time"] = 0.
-default["wfreq_control"]["ecut_spectralf"] = [-2.,1.] 
+default["wfreq_control"]["ecut_spectralf"] = [-2., 1.] 
 default["wfreq_control"]["n_spectralf"] = 204
 # westpp_control
 default["westpp_control"] = {}
 default["westpp_control"]["westpp_calculation"] = "r"
-default["westpp_control"]["westpp_range"] = [1,2]
+default["westpp_control"]["westpp_range"] = [1, 2]
 default["westpp_control"]["westpp_format"] = "C"
 default["westpp_control"]["westpp_sign"] = False
 default["westpp_control"]["westpp_n_pdep_eigen_to_use"] = 1
-default["westpp_control"]["westpp_r0"] = [0.,0.,0.]
+default["westpp_control"]["westpp_r0"] = [0., 0., 0.]
 default["westpp_control"]["westpp_nr"] = 100
 default["westpp_control"]["westpp_rmax"] = 1.
 default["westpp_control"]["westpp_epsinfty"] = 1.
@@ -78,22 +79,17 @@ def update_default_values(key,kwargs) :
        #
        assert("nelec") in kwargs.keys()
        nelec = kwargs["nelec"] 
-       default[key]["n_pdep_eigen"] = nelec
+       default[key]["n_pdep_eigen"] = int(nelec)
     #
     if key == "wfreq_control" :
        #
        assert("nelec") in kwargs.keys()
        nelec = kwargs["nelec"] 
-       default[key]["n_pdep_eigen_to_use"] = nelec
+       default[key]["n_pdep_eigen_to_use"] = int(nelec)
        #
        assert("ecutrho") in kwargs.keys()
        ecutrho = kwargs["ecutrho"] 
        default[key]["ecut_imfreq"] = ecutrho
-       #
-       assert("eksmax") in kwargs.keys()
-       eksmax = kwargs["eksmax"] 
-       default[key]["ecut_refreq"] = eksmax + 0.5
-       default[key]["n_refreq"] = int( default[key]["ecut_refreq"] * rytoev / 0.1 ) 
 
 ################
 # OPEN & PARSE #
@@ -206,6 +202,7 @@ def read_keyword_from_file(*args, **kwargs):
     #
     fileName = args[0]
     keyword = args[1] 
+    verbose = args[2]
     #
     # Assign static & dynamical defaults 
     # 
@@ -226,7 +223,8 @@ def read_keyword_from_file(*args, **kwargs):
     #
     # Print
     #
-    print_dict(keyword, data)
+    if (verbose) : 
+       print_dict(keyword, data)
     #
     return data
 
@@ -249,10 +247,10 @@ wstat_control :
    unknown_key : value # this line will be read but not passed 
 """)
     #
-    read_keyword_from_file(fileName,"input_west")
-    read_keyword_from_file(fileName,"wstat_control",nq=20,nelec=10)
-    read_keyword_from_file(fileName,"wfreq_control",nelec=10,ecutrho=30.,eksmax=2.)
-    read_keyword_from_file(fileName,"westpp_control")
+    read_keyword_from_file(fileName,"input_west",True)
+    read_keyword_from_file(fileName,"wstat_control",True,nq=20,nelec=10)
+    read_keyword_from_file(fileName,"wfreq_control",True,nelec=10,ecutrho=30.)
+    read_keyword_from_file(fileName,"westpp_control",True)
     #
     remove(fileName)
 

Pytools/utils.py

+#!/usr/bin/python3
+
+from __future__ import print_function
+from os import mkdir 
+import sys
+
+#############
+# INTERFACE #
+#############
+
+def my_mkdir(*args, **kwargs):
+    #
+    path = args[0]
+    #
+    try:
+        mkdir(path)
+    except OSError:
+        #print (f"Creation of the directory {path} failed")
+        pass
+    else:
+        #print (f"Successfully created the directory {path} ")
+        pass
+    sys.stdout.flush()
+
+########
+# TEST #
+########
+
+def test() :
+    #
+    dirname = "./wstat.save"
+    #
+    my_mkdir(dirname)
+
+if __name__ == "__main__":
+    # execute only if run as a script
+    test()
+

Tools/Makefile

@@ -16,9 +16,9 @@ IFLAGS=
 TOOLS_OBJS = \
 conversions.o \
 io_push.o \
-logfile.o \
-fetch_input.o \
+my_mkdir.o \
 set_dirs.o \
+fetch_input.o \
 west_print_clocks.o \
 exx_go.o \
 exx_ungo.o \

Tools/fetch_input.py

-#!/usr/bin/python3
-
-# File: fetch_input.py
-# Test: python3 fetch_input.py
-
-from __future__ import print_function
-import sys
-import os
-import yaml
-import json
-
-#########################
-# STATIC DEFAULT VALUES #
-#########################
-
-default = {}
-# input_west
-default["input_west"] = {}
-default["input_west"]["qe_prefix"] = "pwscf"
-default["input_west"]["west_prefix"] = "west"
-default["input_west"]["outdir"] = "./"
-# wstat_control
-default["wstat_control"] = {}
-default["wstat_control"]["wstat_calculation"] = "S"
-default["wstat_control"]["n_pdep_eigen"] = 1
-default["wstat_control"]["n_pdep_times"] = 4
-default["wstat_control"]["n_pdep_maxiter"] = 100
-default["wstat_control"]["n_dfpt_maxiter"] = 250
-default["wstat_control"]["n_pdep_read_from_file"] = 0
-default["wstat_control"]["trev_pdep"] = 1.e-3
-default["wstat_control"]["trev_pdep_rel"] = 1.e-1
-default["wstat_control"]["tr2_dfpt"] = 1.e-12
-default["wstat_control"]["l_kinetic_only"] = False
-default["wstat_control"]["l_minimize_exx_if_active"] = False
-default["wstat_control"]["l_use_ecutrho"] = False
-default["wstat_control"]["qlist"] = [ 1 ]
-
-############################
-# DYNAMICAL DEFAULT VALUES #
-############################
-
-def update_default_values(key,kwargs) :
-    assert key in default.keys()
-    #
-    if key == "wstat_control" :
-       assert("nq") in kwargs.keys()
-       nq = kwargs["nq"] 
-       default[key]["qlist"] = [ i+1 for i in range(nq) ]
-
-def open_and_parse_file(fileName="west.in") :
-    """Opens a file and parses it using the YAML sintax 
-
-    :param fileName: name of the file
-    :type fileName: ``string``
-    :return: parsed data
-    :rtype: ``dict``
-
-    """
-    data = {}
-    try : 
-       with open(fileName, 'r') as stream:
-           try:
-              data = yaml.load(stream,Loader=yaml.SafeLoader)
-           except:
-              print("Cannot parse file")
-    except : 
-       print("Cannot open file : ",fileName)
-    #
-    return data
-
-def print_bar(prefix="",nmarks=92) : 
-    """Prints bar.
-
-    :param prefix: prefix
-    :type prefix: ``string``
-    :param nmarks: number of marks
-    :type nmarks: ``int``
-    """
-    #
-    s = prefix
-    for i in range(nmarks) : 
-       s+="-"
-    print(s)
-
-def check_dict(parsed_data={}, default_data={}) : 
-    """Check data: returns a dictionary with the same keys of default_data. If keys are matching, values of default_data are replaced with those of parsed_data. 
-
-    :param parsed_data: parsed data 
-    :type parsed_data: ``dict``
-    :param default_data: default data 
-    :type default_data: ``dict``
-    :return: checked data
-    :rtype: ``dict``
-
-    """
-    #
-    data = {}
-    #
-    for key in default_data.keys() : 
-        if key in parsed_data.keys() : 
-           data[key] = parsed_data[key]
-        else : 
-           data[key] = default_data[key]
-    #
-    return data
-
-def print_dict(title="input_west", data={}) : 
-    """Prints data.  
-
-    :param title: title
-    :type title: ``string``
-    :param data: data to print
-    :type default_data: ``dict``
-
-    """
-    #
-    nmarks = 92
-    nspaces = 5 
-    s = ""
-    for i in range(nspaces) : 
-       s+=" "
-    #
-    print_bar(s,nmarks)
-    print(s+"I/O Summary : "+str(title))
-    print_bar(s,nmarks)
-    for key in data.keys() :
-       print(s+key,"=",data[key])
-    print_bar(s,nmarks)
-    sys.stdout.flush()
-
-def read_keyword_from_file(*args, **kwargs):
-    """Read keyword from file  
-
-    :return: read data
-    :rtype: ``dict``
-
-    """
-    #
-    fileName = args[0]
-    keyword = args[1] 
-    #
-    parsed_data = open_and_parse_file(fileName)[keyword]
-    default_data = default[keyword]
-    #
-    update_default_values(keyword,kwargs) 
-    #
-    data = check_dict( parsed_data, default_data )
-    #
-    print_dict(keyword, data)
-    #
-    return data
-
-def test() :
-    #
-    fileName = "west.in"
-    #
-    with open(fileName, "w") as file :
-       file.write("""
-input_west : 
-   qe_prefix : molecule
-   west_prefix : molecule
-   outdir : "./"
-wstat_control : 
-   wstat_calculation : R
-""")
-    #
-    read_keyword_from_file(fileName,"input_west")
-    read_keyword_from_file(fileName,"wstat_control",nq=20)
-    #
-    os.remove(fileName)
-
-if __name__ == "__main__":
-    # execute only if run as a script
-    test()
-

IO_kernel/my_mkdir.f90 → Tools/my_mkdir.f90

@@ -14,10 +14,16 @@
 SUBROUTINE my_mkdir( dirname )
   !------------------------------------------------------------------------
   !
-  USE wrappers,  ONLY : f_mkdir_safe
+!  USE wrappers,  ONLY : f_mkdir_safe
   USE mp,        ONLY : mp_barrier,mp_bcast
   USE mp_world,  ONLY : mpime, root, world_comm
-  USE io_files,  ONLY : check_writable
+!  USE io_files,  ONLY : check_writable
+   USE forpy_mod,  ONLY: call_py, call_py_noret, import_py, module_py
+   USE forpy_mod,  ONLY: tuple, tuple_create
+   USE forpy_mod,  ONLY: dict, dict_create
+   USE forpy_mod,  ONLY: list, list_create
+   USE forpy_mod,  ONLY: object, cast
+   USE forpy_mod,  ONLY: exception_matches, KeyError, err_clear, err_print
   !
   ! I/O
   !
@@ -27,24 +33,43 @@ SUBROUTINE my_mkdir( dirname )
   !
   INTEGER                    :: ierr
   CHARACTER(LEN=6), EXTERNAL :: int_to_char
+   TYPE(tuple) :: args
+   TYPE(dict) :: kwargs
+   TYPE(module_py) :: pymod
   !
   ! BARRIER
   !
-  !
-  IF ( mpime == root ) ierr = f_mkdir_safe( TRIM( dirname ) )
-  CALL mp_bcast ( ierr, root, world_comm )
-  !
-  CALL errore( 'create_directory', &
-               'unable to create directory ' // TRIM( dirname ), ierr )
-  !
-  ! ... check whether the scratch directory is writable
-  !
-  IF ( mpime == root ) ierr = check_writable ( dirname, mpime )
-  CALL mp_bcast( ierr, root, world_comm )
-  !
-  CALL errore( 'create_directory:', &
-               TRIM( dirname ) // ' non existent or non writable', ierr )
-  CALL mp_barrier( world_comm )
+  IF ( mpime == root ) THEN 
+       !
+      IERR = import_py(pymod, "utils")
+      !  
+      IERR = tuple_create(args, 1)
+      IERR = args%setitem(0, TRIM(ADJUSTL(dirname)) )
+      IERR = dict_create(kwargs)
+
+      IERR = call_py_noret(pymod, "my_mkdir", args, kwargs)
+      !
+      CALL kwargs%destroy
+      CALL args%destroy
+      CALL pymod%destroy
+
+  ENDIF 
+  CALL mp_barrier(world_comm)
+
+!  IF ( mpime == root ) ierr = f_mkdir_safe( TRIM( dirname ) )
+!  CALL mp_bcast ( ierr, root, world_comm )
+!  !
+!  CALL errore( 'create_directory', &
+!               'unable to create directory ' // TRIM( dirname ), ierr )
+!  !
+!  ! ... check whether the scratch directory is writable
+!  !
+!  IF ( mpime == root ) ierr = check_writable ( dirname, mpime )
+!  CALL mp_bcast( ierr, root, world_comm )
+!  !
+!  CALL errore( 'create_directory:', &
+!               TRIM( dirname ) // ' non existent or non writable', ierr )
+!  CALL mp_barrier( world_comm )
   !
   RETURN
   !

Tools/west_environment.f90

@@ -38,7 +38,7 @@ CONTAINS
     USE base64_module,   ONLY : base64_init 
     USE json_string_utilities, ONLY : lowercase_string
     USE west_version,    ONLY : start_forpy
-    USE logfile_mod,     ONLY : clear_log
+    !USE logfile_mod,     ONLY : clear_log
     !
     CHARACTER(LEN=*), INTENT(IN) :: code
     !
@@ -54,15 +54,16 @@ CONTAINS
 #if defined(__INTEL_COMPILER)
     CALL remove_stack_limit ( )
 #endif
+    CALL start_forpy() 
     !
     ! Input from (-i), output from (-o)
     !
     CALL parse_command_arguments()
-    CALL fetch_input(1,(/1/),.FALSE.)
+    CALL fetch_input_yml(1,(/1/),.FALSE.,.FALSE.)
     !
-    savedir = TRIM(outdir) // trim(west_prefix) // "." // TRIM(lowercase_string(code)) // ".save/"
-    CALL my_mkdir( savedir )
-    logfile = TRIM(savedir) // TRIM(lowercase_string(code))//".log.xml"
+    savedir = TRIM(ADJUSTL(outdir)) // TRIM(ADJUSTL(west_prefix)) // "." // TRIM(lowercase_string(code)) // ".save/"
+    logfile = TRIM(ADJUSTL(savedir)) // TRIM(lowercase_string(code))//".json"
+    CALL my_mkdir( TRIM(ADJUSTL(savedir)) ) 
     !
     ! ... use ".FALSE." to disable all clocks except the total cpu time clock
     ! ... use ".TRUE."  to enable clocks
@@ -116,9 +117,8 @@ CONTAINS
     !
     ! Initialize base64 tables  
     CALL base64_init()
-    CALL start_forpy() 
     !
-    CALL clear_log()
+    !CALL clear_log()
     CALL west_opening_message( code )
 #if defined(__MPI)
     CALL report_parallel_status ( )
@@ -196,7 +196,7 @@ CONTAINS
   !
   SUBROUTINE west_opening_message( code )
     !
-    !USE json_module,     ONLY : json_file
+    USE json_module,     ONLY : json_file
     USE io_global,       ONLY : stdout
     USE global_version,  ONLY : version_number, svn_revision
     USE west_version,    ONLY : west_version_number, west_git_revision
@@ -204,7 +204,7 @@ CONTAINS
     USE westcom,         ONLY : logfile
     USE base64_module,   ONLY : islittleendian  
     USE forpy_mod,        ONLY : dict, dict_create 
-    USE logfile_mod,      ONLY : append_log, itoa, ltoa, dtoa
+    !USE logfile_mod,      ONLY : append_log, itoa, ltoa, dtoa
     !
     ! I/O
     !
@@ -212,8 +212,8 @@ CONTAINS
     !
     ! Workspace
     !
-    !TYPE(json_file) :: json
-    !INTEGER :: iunit
+    TYPE(json_file) :: json
+    INTEGER :: iunit
     CHARACTER(LEN=9)  :: cdate, ctime
     !
     INTEGER :: IERR
@@ -249,50 +249,50 @@ CONTAINS
     ENDIF 
     !
     IF( mpime == root ) THEN 
-       !
-      !CALL json%initialize()
-      !!
-      !CALL json%add('runjob.startdate', TRIM(cdate) )
-      !CALL json%add('runjob.starttime', TRIM(ctime) )
-      !CALL json%add('runjob.completed', .FALSE. )
-      !CALL json%add('software.package', "WEST" )
-      !CALL json%add('software.program', TRIM(code) )
-      !CALL json%add('software.version', TRIM(west_version_number) )
-      !IF( TRIM (west_git_revision) /= "unknown" ) CALL json%add('software.westgit', TRIM(west_git_revision) )
-      !CALL json%add('software.website',"http://www.west-code.org")
-      !CALL json%add('software.citation',"M. Govoni et al., J. Chem. Theory Comput. 11, 2680 (2015).")
-      !CALL json%add('software.qeversion', TRIM(version_number) )
-      !IF( TRIM (svn_revision) /= "unknown" ) CALL json%add('software.qesvn', TRIM(svn_revision) )
-      !CALL json%add('config.io.islittleendian', islittleendian() )
-      !!
-      !OPEN( NEWUNIT=iunit, FILE=TRIM(logfile) )
-      !CALL json%print_file( iunit )
-      !CLOSE( iunit )
-      !!
-      !CALL json%destroy()
+      ! 
+      CALL json%initialize()
       !
-      s = '{ '
-      s = s // '"startdate" : '   //'"'//TRIM(cdate) //'" , '
-      s = s // '"startime" : '    //'"'//TRIM(ctime)     //'" , '
-      s = s // '"package" : '     //'"WEST"'          //' , '
-      s = s // '"program" : '     //'"'//TRIM(code)      //'" , '
-      s = s // '"version" : '     //'"'//TRIM(west_version_number) //'" , '
-      IF( TRIM (west_git_revision) /= "unknown" ) THEN
-         s = s // '"git_version" : ' //'"'//TRIM(west_git_revision) //'" , '
-      ENDIF
-      s = s // '"website" : '     //'"http://www.west-code.org"' //' , '
-      s = s // '"citation" : '    //'"M. Govoni et al., J. Chem. Theory Comput. 11, 2680 (2015)."' //' , '
-      s = s // '"website" : '     //'"http://www.west-code.org"' //' , '
-      s = s // '"qeversion" : '     //'"'//TRIM(version_number) //'" , '
-      s = s // '"islittleendian" : ' //ltoa(islittleendian()) //'   '
-      s = s // '}'
+      CALL json%add('runjob.startdate', TRIM(cdate) )
+      CALL json%add('runjob.starttime', TRIM(ctime) )
+      CALL json%add('runjob.completed', .FALSE. )
+      CALL json%add('software.package', "WEST" )
+      CALL json%add('software.program', TRIM(code) )
+      CALL json%add('software.version', TRIM(west_version_number) )
+      IF( TRIM (west_git_revision) /= "unknown" ) CALL json%add('software.westgit', TRIM(west_git_revision) )
+      CALL json%add('software.website',"http://www.west-code.org")
+      CALL json%add('software.citation',"M. Govoni et al., J. Chem. Theory Comput. 11, 2680 (2015).")
+      CALL json%add('software.qeversion', TRIM(version_number) )
+      IF( TRIM (svn_revision) /= "unknown" ) CALL json%add('software.qesvn', TRIM(svn_revision) )
+      CALL json%add('config.io.islittleendian', islittleendian() )
       !
-      IERR = dict_create(attr)
-      IERR = attr%setitem("type", "intro" )
+      OPEN( NEWUNIT=iunit, FILE=TRIM(logfile) )
+      CALL json%print_file( iunit )
+      CLOSE( iunit )
       !
-      CALL append_log( s, attr )
+      CALL json%destroy()
       !
-      CALL attr%destroy
+      !s = '{ '
+