Nexus: Move all log() functions to nxs_print() for future use of logging library

nexus/nexus/__init__.py

@@ -29,8 +29,7 @@
 from pathlib import Path
 
 from .nexus_version import nexus_version
-from .generic       import generic_settings
-from .developer     import obj, log, NexusError
+from .developer     import obj, nxs_print, NexusError
 from .debug         import ci
 from .utilities     import path_string
 
@@ -218,7 +217,7 @@ def __call__(self,**kwargs):
         write_splash()
 
         # print version information
-        self.log("Checking current machine for Nexus dependencies...\n")
+        self.nxs_print("Checking current machine for Nexus dependencies...\n")
         pkg_sort = {
             "numpy":      0,
             "scipy":      1,
@@ -293,9 +292,9 @@ def __call__(self,**kwargs):
 
         version_text += "\n"
 
-        self.log(version_text)
+        self.nxs_print(version_text)
 
-        self.log('Applying user settings')
+        self.nxs_print('Applying user settings')
 
         # assign simple variables
         for name in Settings.core_assign_vars:
@@ -505,9 +504,9 @@ def process_machine_settings(self,mset):
         if 'machine' in mset:
             machine_name = mset.machine
             if machine_name in {"ws", "workstation"}:
-                self.log("Automatically detecting physical CPU cores for workstation...", n=1)
+                self.nxs_print("Automatically detecting physical CPU cores for workstation...", n=1)
                 n_cores = get_cpu_cores()
-                self.log(f"Using {n_cores} core workstation", n=1)
+                self.nxs_print(f"Using {n_cores} core workstation", n=1)
                 machine_name = f"ws{n_cores}"
 
                 if not Machine.exists(machine_name):

nexus/nexus/basisset.py

@@ -9,7 +9,7 @@
 from types import MappingProxyType
 import numpy as np
 from .periodic_table import Elements
-from .developer import DevBase, obj, log, NexusError
+from .developer import DevBase, obj, nxs_print, NexusError
 from .fileio import TextFile
 from .utilities import path_string, to_str
 
@@ -64,11 +64,11 @@ def readbs(self,*bsfiles):
             bsfiles = bsfiles[0]
         #end if
         bss = []
-        log('')
-        log('  Basissets')
+        nxs_print('')
+        nxs_print('  Basissets')
         for filepath in bsfiles:
             filepath_str = str(filepath)
-            log('    reading basis: '+filepath_str)
+            nxs_print('    reading basis: '+filepath_str)
             ext = filepath_str.split('.')[-1].lower()
             if ext=='gms_bas' or ext=='bas':
                 bs = gamessBasisFile(filepath_str)
@@ -77,7 +77,7 @@ def readbs(self,*bsfiles):
             #end if
             bss.append(bs)
         #end for
-        log('')
+        nxs_print('')
         self.addbs(bss)
     #end def readbs
 

nexus/nexus/bin/qdens

@@ -200,7 +200,7 @@ class QDBase(DevBase):
 
     def vlog(self,*args,**kwargs):
         if self.verbose:
-            DevBase.log(self,*args,**kwargs)
+            DevBase.nxs_print(self,*args,**kwargs)
         #end if
     #end def vlog
 
@@ -210,7 +210,7 @@ class QDBase(DevBase):
     #end def vmlog
 
     def help(self):
-        self.log('\n'+self.parser.format_help().strip()+'\n')
+        self.nxs_print('\n'+self.parser.format_help().strip()+'\n')
     #end def help
 
     # options accessor functions
@@ -1213,8 +1213,8 @@ class QMCDensityProcessor(QDBase):
         self.vlog(f'\n{self.name} initializing')
 
         if self.verbose:
-            self.log('\noptions provided:')
-            self.log(str(self.options))
+            self.nxs_print('\noptions provided:')
+            self.nxs_print(str(self.options))
         #end if
 
 
@@ -1496,7 +1496,7 @@ class QMCDensityProcessor(QDBase):
         #end if
 
         if opt.verbose and opt.input_metadata is not None:
-            self.log(f'input density metadata found for series: {sorted(opt.input_metadata.series.keys())}')
+            self.nxs_print(f'input density metadata found for series: {sorted(opt.input_metadata.series.keys())}')
         #end if
 
         for file in files_in:

nexus/nexus/bin/qdens-radial

@@ -97,7 +97,7 @@ class QDRBase(DevBase):
 
     def vlog(self,*args,**kwargs):
         if self.verbose:
-            DevBase.log(self,*args,**kwargs)
+            DevBase.nxs_print(self,*args,**kwargs)
         #end if
     #end def vlog
 
@@ -107,7 +107,7 @@ class QDRBase(DevBase):
     #end def vmlog
 
     def help(self):
-        self.log('\n'+self.parser.format_help().strip()+'\n')
+        self.nxs_print('\n'+self.parser.format_help().strip()+'\n')
     #end def help
 
 #end class QDBase
@@ -305,7 +305,7 @@ class QMCDensityRadialProcessor(QDRBase):
         # if VMC file is given, perform extrapolation before 
         # instantiating ChargeDensity object
         if opt.vmc_file is not None:
-            self.log('Extrapolating from VMC and DMC densities...')
+            self.nxs_print('Extrapolating from VMC and DMC densities...')
             vmc_xsf_data = XsfFile(filepath=opt.vmc_file)
             dmc_xsf_data = XsfFile(filepath=file)
             # Initialize extrapolated XsfFile object
@@ -319,14 +319,14 @@ class QMCDensityRadialProcessor(QDRBase):
             dmc_xsf_data = XsfFile(filepath=file)
             file = deepcopy(dmc_xsf_data)
             if opt.write_extrap:
-                self.log('\nWARNING: You provided --write, however, extrapolated density will not be written since a VMC file was not provided (via --vmc=VMC_FILE).\n')
+                self.nxs_print('\nWARNING: You provided --write, however, extrapolated density will not be written since a VMC file was not provided (via --vmc=VMC_FILE).\n')
             #end if
         #end if
 
         show_error=False
         # If error files are given, then user wants resampled error bars
         if opt.dmc_err_file is not None:
-            self.log('Resampling to obtain error bar (NOTE: This can be slow)...')
+            self.nxs_print('Resampling to obtain error bar (NOTE: This can be slow)...')
             if opt.vmc_file is not None and opt.vmc_err_file is not None:
                 # Data without errors
                 vmc_xsf_data = XsfFile(filepath=opt.vmc_file)
@@ -381,9 +381,9 @@ class QMCDensityRadialProcessor(QDRBase):
             #end if
 
             nsamples = opt.nsamples
-            self.log(f'Will compute {nsamples} samples...')
+            self.nxs_print(f'Will compute {nsamples} samples...')
             for i in range(nsamples):
-                self.log(f'sample: {i}')
+                self.nxs_print(f'sample: {i}')
                 resample_xsf_data = deepcopy(file)
                 for d1_idx, d1 in enumerate(file.data[3]['density']['density'].values):
                     for d2_idx, d2 in enumerate(d1):
@@ -500,7 +500,7 @@ class QMCDensityRadialProcessor(QDRBase):
             cd.set_attribute('density_units','A') # xsf format uses Angstrom units which makes the QMCPACK density units (e/Angstrom^3) after volume normalization
         #end if
 
-        self.log('\nNorm:',cd.norm())
+        self.nxs_print('\nNorm:',cd.norm())
 
         if opt.plot:
             if opt.species is None:
@@ -534,9 +534,9 @@ class QMCDensityRadialProcessor(QDRBase):
                     r = opt.radii[0]
                 #end if
                 if not show_error:
-                    self.log(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f}\n')
+                    self.nxs_print(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f}\n')
                 else:
-                    self.log(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f} +/- {std_dict[at]:.8f}\n')
+                    self.nxs_print(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f} +/- {std_dict[at]:.8f}\n')
                 #end if
             #end for
         else:
@@ -549,9 +549,9 @@ class QMCDensityRadialProcessor(QDRBase):
                     r = opt.radii[0]
                 #end if
                 if not show_error:
-                    self.log(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f}\n')
+                    self.nxs_print(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f}\n')
                 else:
-                    self.log(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f} +/- {std_dict[at]:.8f}\n')
+                    self.nxs_print(f'{cstr} Value of {at} Species at Cutoff {r} is: {rdens.tot[at].density[-1]:.8f} +/- {std_dict[at]:.8f}\n')
                 #end if
             #end for
         #end if

nexus/nexus/bin/qmc-fit

@@ -85,7 +85,7 @@ def find_nexus_modules():
 
 # Load Nexus modules
 find_nexus_modules()
-from nexus.developer import obj,log
+from nexus.developer import obj,nxs_print
 from nexus.numerics import jackknife,jackknife_aux
 from nexus.numerics import simstats,equilibration_length
 from nexus.numerics import curve_fit,least_squares
@@ -424,7 +424,7 @@ def timestep_fit(args):
     scalar_files = sorted(opt.scalar_files)
 
     if len(scalar_files)==0:
-        log('\n'+parser.format_help().strip()+'\n')
+        nxs_print('\n'+parser.format_help().strip()+'\n')
         sys.exit()
     #end if
 
@@ -472,11 +472,11 @@ def timestep_fit(args):
         pvals.append('({0} +/- {1})'.format(*stat_strings(pmean[n],perror[n])))
     #end for
 
-    log('\nfit function  : '+opt.fit_function)
-    log('fitted formula: '+func_info.format.format(*pvals))
+    nxs_print('\nfit function  : '+opt.fit_function)
+    nxs_print('fitted formula: '+func_info.format.format(*pvals))
     for pname,pfunc in func_info.params:  # noqa: B007
         pm,pe = stat_strings(*auxres[pname])
-        log(f'{pname:<14}: {pm} +/- {pe}  Ha\n')
+        nxs_print(f'{pname:<14}: {pm} +/- {pe}  Ha\n')
     #end for
 
     # plot the fit (if available)
@@ -546,7 +546,7 @@ def hubbard_u_fit(args):
         #end if
         x = opt.exx
     else:
-        log("\n Please provide either EXX or Hubbard_U values")
+        nxs_print("\n Please provide either EXX or Hubbard_U values")
     #end if
 
     parse_list(opt,'equils',int,len1=True)
@@ -562,8 +562,8 @@ def hubbard_u_fit(args):
         pvals.append('({0} +/- {1})'.format(*stat_strings(pmean[n],perror[n])))
     #end for
 
-    log('\nfit function  : '+opt.fit_function)
-    log('fitted formula: '+func_info.format.format(*pvals))
+    nxs_print('\nfit function  : '+opt.fit_function)
+    nxs_print('fitted formula: '+func_info.format.format(*pvals))
     for pname,pfunc in func_info.params:  # noqa: B007
         for i in range(len(auxres[pname][0])):
             pm,pe = stat_strings(*np.array(auxres[pname])[:,i])
@@ -581,7 +581,7 @@ def hubbard_u_fit(args):
             else:
                 param = pname
             #end if
-            log(f'root {i+1} {param:<14}: {pm} +/- {pe} {unit}')
+            nxs_print(f'root {i+1} {param:<14}: {pm} +/- {pe} {unit}')
     #end for
     # plot the fit (if available)
 
@@ -657,13 +657,13 @@ def eos_fit(args):
     for n in range(len(pmean)):
         pvals.append('({0} +/- {1})'.format(*stat_strings(pmean[n],perror[n])))
     #end for
-    log('\nfit function  : '+opt.fit_function)
-    log('fitted formula: '+func_info.format.format(*pvals))
+    nxs_print('\nfit function  : '+opt.fit_function)
+    nxs_print('fitted formula: '+func_info.format.format(*pvals))
 
     if 'params' in func_info.keys():
         for pname,pfunc in func_info.params:  # noqa: B007
             pm,pe = stat_strings(*np.array(auxres[pname]))
-            log(f'{pname}: {pm} +/- {pe} ')
+            nxs_print(f'{pname}: {pm} +/- {pe} ')
         #end for
 
     # plot the fit (if available)
@@ -751,7 +751,7 @@ if __name__=='__main__':
     fit_types = sorted(all_fit_functions.keys())
     parser, args = parse_args()
     if len(args.scalar_files) == 0:
-        log('\n'+'Please provide scalar files'+'\n')
+        nxs_print('\n'+'Please provide scalar files'+'\n')
         parser.print_help()
         sys.exit()
     #end if

nexus/nexus/bin/qmca

@@ -213,7 +213,7 @@ class QBase(DevBase):
             text+=str(t)+' '
         #end for
         pad = n*'  '
-        self._logfile.write(pad+text.replace('\n','\n'+pad)+'\n')
+        sys.stdout.write(pad+text.replace('\n','\n'+pad)+'\n')
     #end def log
 
 

nexus/nexus/developer.py

@@ -27,11 +27,10 @@
 
 
 from .generic import NexusError, FileFormatError, NotAnElementError  # noqa: F401
-from .generic import error, log, warn, message  # noqa: F401
+from .generic import error, nxs_print, warn, message  # noqa: F401
 
 
 import traceback
-from .generic import generic_settings
 
 
 def deprecation_error():
@@ -58,15 +57,9 @@ def __iter__(self): deprecation_error()
     # change from deepcopy to shallow copy, blow up
     def copy(self): deprecation_error()
 
-    # logging - unique to Nexus-style DevBase (future refactor)
-    @property
-    def _logfile(self):
-        return generic_settings.devlog
 
-
-    def log(self,*a,**kw):
-        kw.setdefault('logfile',self._logfile)
-        log(*a,**kw)
+    def nxs_print(self,*a,**kw):
+        nxs_print(*a,**kw)
 
     def warn(self,msg,indent='    '):
         warn(

nexus/nexus/examples/quantum_espresso/01_diamond_scf/diamond_lda.py

@@ -7,8 +7,8 @@
 settings(
     pseudo_dir = '../pseudopotentials',
     results    = '',
-    sleep      = 3,
-    machine    = 'ws16',
+    sleep      = 0.5,
+    machine    = 'ws8',
     )
 
 system = generate_physical_system(
@@ -26,7 +26,7 @@
 scf = generate_pwscf(
     identifier   = 'scf',
     path         = 'diamond/scf',
-    job          = job(cores=16,app='pw.x'),
+    job          = job(cores=6,app='pw.x'),
     input_type   = 'generic',
     calculation  = 'scf',
     input_dft    = 'lda',