Update to python3

examples/AB_model.py

@@ -40,7 +40,7 @@ def main():
     parameters['E_react'] = {'value': 0.9}
 
 
-    for key, value in parameters.iteritems():
+    for key, value in parameters.items():
         pt.add_parameter(name=key, **value)
 
 

kmos/__init__.py

@@ -73,7 +73,7 @@ def evaluate_rate_expression(rate_expr, parameters={}):
         parameters = [Parameter(), ... ]
      """
     import tokenize
-    import StringIO
+    from io import StringIO
     import math
     from kmos import units
 
@@ -90,10 +90,10 @@ def evaluate_rate_expression(rate_expr, parameters={}):
         replaced_tokens = []
 
         # replace some aliases
-        for old, new in rate_aliases.iteritems():
+        for old, new in rate_aliases.items():
             rate_expr = rate_expr.replace(old, new)
         try:
-            input = StringIO.StringIO(rate_expr).readline
+            input = StringIO(rate_expr).readline
             tokens = list(tokenize.generate_tokens(input))
         except:
             raise Exception('Could not tokenize expression: %s' % input)
@@ -103,7 +103,7 @@ def evaluate_rate_expression(rate_expr, parameters={}):
             elif token in dir(units):
                 replaced_tokens.append((i, str(eval('units.' + token))))
             elif token.startswith('m_'):
-                from ase.atoms import string2symbols
+                from ase.symbols import string2symbols
                 from ase.data import atomic_masses
                 from ase.data import atomic_numbers
                 species_name = '_'.join(token.split('_')[1:])
@@ -146,7 +146,7 @@ def evaluate_rate_expression(rate_expr, parameters={}):
         rate_expr = tokenize.untokenize(replaced_tokens)
         try:
             rate_const = eval(rate_expr)
-        except Exception, e:
+        except Exception as e:
             raise UserWarning(
             "Could not evaluate rate expression: %s\nException: %s" \
                 % (rate_expr, e))

kmos/cli.py

@@ -39,10 +39,12 @@
 #    You should have received a copy of the GNU General Public License
 #    along with kmos.  If not, see <http://www.gnu.org/licenses/>.
 
-from __future__ import with_statement
+import logging
 import os
 import shutil
 
+logger = logging.getLogger(__name__)
+
 usage = {}
 usage['all'] = """kmos help all
     Display documentation for all commands.
@@ -212,13 +214,19 @@ def get_options(args=None, get_parser=False):
                       default=False,
                       )
 
-    try:
-        from numpy.distutils.fcompiler import get_default_fcompiler
-        from numpy.distutils import log
-        log.set_verbosity(-1, True)
-        fcompiler = get_default_fcompiler()
-    except:
-        fcompiler = 'gfortran'
+    # Detect available Fortran compiler
+    # Note: numpy.distutils is deprecated and removed in Python >= 3.12
+    # Using direct detection instead
+    import shutil
+    fcompiler = 'gnu95'  # Default: gnu95 is the f2py name for gfortran
+
+    # Try to detect available Fortran compiler
+    if shutil.which('gfortran'):
+        fcompiler = 'gnu95'
+    elif shutil.which('ifort'):
+        fcompiler = 'intel'
+    elif shutil.which('ifx'):
+        fcompiler = 'intelem'
 
     parser.add_option('-f', '--fcompiler',
                       dest='fcompiler',
@@ -287,9 +295,9 @@ def main(args=None):
             model.do_steps(nsteps)
 
         needed_time = time() - time0
-        print('Using the [%s] backend.' % model.get_backend())
-        print('%s steps took %.2f seconds' % (nsteps, needed_time))
-        print('Or %.2e steps/s' % (1e6 / needed_time))
+        logger.info('Using the [%s] backend.' % model.get_backend())
+        logger.info('%s steps took %.2f seconds' % (nsteps, needed_time))
+        logger.info('Or %.2e steps/s' % (1e6 / needed_time))
         model.deallocate()
     elif args[0] == 'build':
         from kmos.utils import build
@@ -306,7 +314,7 @@ def main(args=None):
             parser.error('XML file and export path expected.')
         if len(args) < 3:
             out_dir = '%s_%s' % (os.path.splitext(args[1])[0], options.backend)
-            print('No export path provided. Exporting to %s' % out_dir)
+            logger.info('No export path provided. Exporting to %s' % out_dir)
             args.append(out_dir)
 
         xml_file = args[1]
@@ -326,7 +334,7 @@ def main(args=None):
         if len(args) < 3:
             out_dir = '%s_%s' % (os.path.splitext(args[1])[0], options.backend)
 
-            print('No export path provided. Exporting to %s' % out_dir)
+            logger.info('No export path provided. Exporting to %s' % out_dir)
             args.append(out_dir)
 
         xml_file = args[1]
@@ -352,14 +360,14 @@ def main(args=None):
                     if options.overwrite :
                         overwrite = 'y'
                     else:
-                        overwrite = raw_input(('Should I overwrite existing %s ?'
+                        overwrite = input(('Should I overwrite existing %s ?'
                                                '[y/N]  ') % out).lower()
                     if overwrite.startswith('y') :
-                        print('Overwriting {out}'.format(**locals()))
+                        logger.info('Overwriting {out}'.format(**locals()))
                         os.remove('../%s' % out)
                         shutil.move(out, '..')
                     else :
-                        print('Skipping {out}'.format(**locals()))
+                        logger.info('Skipping {out}'.format(**locals()))
                 else:
                     shutil.move(out, '..')
 
@@ -368,7 +376,7 @@ def main(args=None):
         pt = kmos.io.import_file(args[1])
         if len(args) < 3:
             out_dir = os.path.splitext(args[1])[0]
-            print('No export path provided. Exporting kmc_settings.py to %s'
+            logger.info('No export path provided. Exporting kmc_settings.py to %s'
                   % out_dir)
             args.append(out_dir)
 
@@ -384,12 +392,12 @@ def main(args=None):
             parser.error('Which help do you  want?')
         if args[1] == 'all':
             for command in sorted(usage):
-                print(usage[command])
+                logger.info(usage[command])
         elif args[1] in usage:
-            print('Usage: %s\n' % usage[args[1]])
+            logger.info('Usage: %s\n' % usage[args[1]])
         else:
             arg = match_keys(args[1], usage, parser)
-            print('Usage: %s\n' % usage[arg])
+            logger.info('Usage: %s\n' % usage[arg])
 
     elif args[0] == 'import':
         import kmos.io
@@ -403,10 +411,10 @@ def main(args=None):
 
     elif args[0] == 'rebuild':
         from time import sleep
-        print('Will rebuild model from kmc_settings.py in current directory')
-        print('Please do not interrupt,'
+        logger.info('Will rebuild model from kmc_settings.py in current directory')
+        logger.info('Please do not interrupt,'
               ' build process, as you will most likely')
-        print('loose the current model files.')
+        logger.info('loose the current model files.')
         sleep(2.)
         from sys import path
         path.append(os.path.abspath(os.curdir))
@@ -456,17 +464,17 @@ def main(args=None):
         try:
             model = KMC_Model(print_rates=False)
         except:
-            print("Warning: could not import kmc_model!"
+            logger.info("Warning: could not import kmc_model!"
                   " Please make sure you are in the right directory")
         sh(banner='Note: model = KMC_Model(print_rates=False){catmap_message}'.format(**locals()))
         try:
             model.deallocate()
         except:
-            print("Warning: could not deallocate model. Was is allocated?")
+            logger.info("Warning: could not deallocate model. Was is allocated?")
 
     elif args[0] == 'version':
         from kmos import VERSION
-        print(VERSION)
+        logger.info(VERSION)
 
     elif args[0] == 'view':
         from sys import path
@@ -479,7 +487,7 @@ def main(args=None):
         path.append(os.path.abspath(os.curdir))
         from kmos.run import KMC_Model
         model = KMC_Model(banner=False, print_rates=False)
-        print(model.xml())
+        logger.info(model.xml())
 
     else:
         parser.error('Command "%s" not understood.' % args[0])

kmos/fortran_src/assert.ppc

@@ -1,5 +1,5 @@
 #ifdef DEBUG
-#define ASSERT(a, r) if(.not.(a))call assertion_fail(#a ,r)
+#define ASSERT(a, r) if(.not.(a))call assertion_fail("assertion failed" ,r)
 #else
 #define ASSERT(a, r)
 #endif

kmos/fortran_src/base.mpy

@@ -640,8 +640,7 @@
 #@         integ_rates(i)=integ_rates(i)+nr_of_sites(i)*rates(i)*kmc_time_step
 #@     enddo
 #@ 
-#@     ASSERT(accum_rates(nr_of_proc).gt.0.,"base/update_accum_rate found" // &
-#@         "accum_rates(nr_of_proc)=0, so no process is available at all")
+#@     ASSERT(accum_rates(nr_of_proc).gt.0.,"base/update_accum_rate: no process available")
 #@ 
 #@ end subroutine update_integ_rate
 #@ !------ S. Matera 09/18/2012------
@@ -802,20 +801,20 @@
 #@ end subroutine deallocate_system
 #@ 
 #@ 
-#@ pure function get_system_name()
+#@ subroutine get_system_name(output_system_name)
 #@     !****f* base/get_system_name
 #@     ! FUNCTION
 #@     !    Return the systems name, that was specified with base/allocate_system
 #@     !
 #@     ! ARGUMENTS
 #@     !
-#@     !    * ``system_name`` Writeable string of type character(len=200).
+#@     !    * ``output_system_name`` Writeable string of type character(len=200).
 #@     !******
 #@     !---------------I/O variables---------------
-#@     character(len=200) :: get_system_name
-#@ 
-#@     get_system_name = system_name
-#@ end function get_system_name
+#@     character(len=200), intent(out) :: output_system_name
+#@
+#@     output_system_name = system_name
+#@ end subroutine get_system_name
 #@ 
 #@ 
 #@ subroutine set_system_name(input_system_name)

kmos/fortran_src/base_lat_int.mpy

@@ -651,8 +651,7 @@ nr_of_species_m1 =  nr_of_species - 1
 #@         integ_rates(i)=integ_rates(i)+nr_of_sites(i)*rates(i)*kmc_time_step
 #@     enddo
 #@
-#@     ASSERT(accum_rates(nr_of_proc).gt.0.,"base/update_accum_rate found"// &
-#@         "accum_rates(nr_of_proc)=0, so no process is available at all")
+#@     ASSERT(accum_rates(nr_of_proc).gt.0.,"base/update_accum_rate: no process available")
 #@
 #@ end subroutine update_integ_rate
 #@ !------ S. Matera 09/18/2012------
@@ -813,20 +812,20 @@ nr_of_species_m1 =  nr_of_species - 1
 #@ end subroutine deallocate_system
 #@
 #@
-#@ pure function get_system_name()
+#@ subroutine get_system_name(output_system_name)
 #@   !****f* base/get_system_name
 #@   ! FUNCTION
 #@   !    Return the systems name, that was specified with base/allocate_system
 #@   !
 #@   ! ARGUMENTS
 #@   !
-#@   !    * ``system_name`` Writeable string of type character(len=200).
+#@   !    * ``output_system_name`` Writeable string of type character(len=200).
 #@   !******
 #@   !---------------I/O variables---------------
-#@   character(len=200) :: get_system_name
+#@   character(len=200), intent(out) :: output_system_name
 #@
-#@   get_system_name = system_name
-#@ end function get_system_name
+#@   output_system_name = system_name
+#@ end subroutine get_system_name
 #@
 #@
 #@ subroutine set_system_name(input_system_name)

kmos/fortran_src/base_otf.f90

@@ -733,8 +733,7 @@ subroutine update_integ_rate()
         integ_rates(i)=integ_rates(i)+rates_matrix(i,volume+1)*kmc_time_step
     enddo
 
-    ASSERT(accum_rates(nr_of_proc).gt.0.,"base/update_accum_rate found"// &
-        "accum_rates(nr_of_proc)=0, so no process is available at all")
+    ASSERT(accum_rates(nr_of_proc).gt.0.,"base/update_accum_rate: no process available")
 
 end subroutine update_integ_rate
 !------ S. Matera 09/18/2012------
@@ -933,20 +932,20 @@ subroutine deallocate_system()
 end subroutine deallocate_system
 
 
-pure function get_system_name()
+subroutine get_system_name(output_system_name)
   !****f* base/get_system_name
   ! FUNCTION
   !    Return the systems name, that was specified with base/allocate_system
   !
   ! ARGUMENTS
   !
-  !    * ``system_name`` Writeable string of type character(len=200).
+  !    * ``output_system_name`` Writeable string of type character(len=200).
   !******
   !---------------I/O variables---------------
-  character(len=200) :: get_system_name
+  character(len=200), intent(out) :: output_system_name
 
-  get_system_name = system_name
-end function get_system_name
+  output_system_name = system_name
+end subroutine get_system_name
 
 
 subroutine set_system_name(input_system_name)

kmos/gui/__init__.py

@@ -19,7 +19,7 @@
 
 # standard modules
 import optparse
-import StringIO
+from io import StringIO
 import sys
 import os
 
@@ -77,17 +77,17 @@
 def verbose(func):
     """Debugging helper that allows to track input and output of function
     via decoration"""
-    print >> sys.stderr, "monitor %r" % (func.func_name)
+    print("monitor %r" % (func.__name__), file=sys.stderr)
 
     def wrapper_func(*args, **kwargs):
         """The wrapping function
         """
-        print >> sys.stderr, "call(\033[0;31m%s.%s\033[0;30m): %r\n" % \
-                (type(args[0]).__name__, func.func_name, args[1:]), \
-                sys.stderr.flush()
+        print("call(\033[0;31m%s.%s\033[0;30m): %r\n" %
+                (type(args[0]).__name__, func.__name__, args[1:]), file=sys.stderr)
+        sys.stderr.flush()
         ret = func(*args, **kwargs)
-        print >> sys.stderr, "    ret(%s): \033[0;32m%r\033[0;30m\n" % \
-                 (func.func_name, ret)
+        print("    ret(%s): \033[0;32m%r\033[0;30m\n" %
+                 (func.__name__, ret), file=sys.stderr)
         return ret
     return wrapper_func
 
@@ -484,7 +484,7 @@ def __init__(self):
         self.menubar.insert_action_group(actions, 0)
         try:
             mergeid = self.menubar.add_ui_from_string(menu_layout)
-        except gobject.GError, error:
+        except gobject.GError as error:
             print('Building menu failed: %s, %s' % (error, mergeid))
 
         # Initialize the project tree, passing in the menu bar