rotconst naming consistency with main branch

.github/workflows/cclib_pytest.yml

@@ -10,7 +10,11 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        container: ['shivupa/cclib-ci:py36', 'shivupa/cclib-ci:py37', 'shivupa/cclib-ci:py38']
+        container:
+          - 'shivupa/cclib-ci:py37-edge'
+          - 'shivupa/cclib-ci:py38-edge'
+          - 'shivupa/cclib-ci:py39-edge'
+          - 'shivupa/cclib-ci:py310-edge'
     container:
       image: ${{ matrix.container }}
     defaults:
@@ -24,7 +28,7 @@ jobs:
           git config --global --add safe.directory /__w/cclib/cclib
       - name: Prepare conda environment
         run: |
-          echo "/env/bin" >> $GITHUB_PATH
+          echo "/opt/conda/envs/cclib/bin" >> $GITHUB_PATH
       - name: Install cclib
         run: |
           python -m pip install .

ANNOUNCE

@@ -1,6 +1,4 @@
-On behalf of the cclib development team, we are pleased to announce the release of cclib 1.7.1, which is now available for download from https://cclib.github.io. This is a major update to version 1.6.4 that drops support for Python 2, and includes several small improvements.
-
-WARNING: Support for Python 2 is dropped in this version.
+On behalf of the cclib development team, we are pleased to announce the release of cclib 1.7.2, which is now available for download from https://cclib.github.io. This is a minor release with several small changes and improvements.
 
 cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from 15 different programs: ADF, DALTON, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, Molpro, MOLCAS, MOPAC, NWChem, ORCA, Psi, QChem and Turbomole.
 

CHANGELOG

@@ -1,3 +1,17 @@
+Changes in cclib-1.7.2
+
+Features:
+    * Support vibfreqs, vibirs, etenergies, etsyms, etoscs and etsecs for NWChem (BenoitDamota)
+    * Support temperature, pressure, enthalpy, entropy, zpve and electronic_thermal_energy for NWChem (BenoitDamota)
+    * Better metadata support for point group detection
+    * Updated code and test file versions to QChem 5.4 and ORCA 5.0
+
+Bugfixes:
+    * Fixed parsing mpenergies for optimization for Turbomole (Oliver Lee)
+    * Fixed ccenergies for Gaussian (Oliver Lee)
+    * Fixed oscillator strengths for ORCA (Felix Plasser)
+    * Fixed units of parsed MO energies for fchk
+
 Changes in cclib-1.7.1
 
 Features:

THANKS

@@ -1,12 +1,17 @@
 Core developers:
 Eric J. Berquist
+Minsik Cho
+Amanda Dumi
+Felipe S. Schneider
 Geoff Hutchison
 Karol M. Langner
 Noel M. O'Boyle (retired)
 Adam L. Tenderholt
+Shiv Upadhyay
 
 Developers that have added at least ~1K SLOC:
 Sagar Gaur
+Oliver Lee
 Sanjeed Schamnad
 Kunal Sharma
 Casper Steinmann
@@ -17,31 +22,41 @@ Nuno Bandeira -- for bug reporting
 Björn Baumeier -- for bug reporting
 Dermot Brougham -- for bug reporting
 bwang2453 -- for patches and new features
+Javier Cerezo -- for patches
 Avril Coghlan -- for designing the cclib logo
 Ramon Crehuet -- for new features
+Michael D'Addario -- for fixes
 Björn Dahlgren -- for bug reporting
 Yafei Dai -- for bug reporting
 Abhishek Dey -- for bug reporting
 Matt Ernst -- for patches
 Clyde Fare -- for bug reporting and patches
+Elliot Farrar -- for fixes
+froessler -- for cleanups
 Christos Garoufalis -- for bug reporting
 Alessandro Genova - for patches and fixes
-Sagar Gaur -- for patches
 glideht -- for bug reporting
 Edward Holland -- for patches
 Karen Hemelsoet -- for bug reporting
 Ian Hovell -- for bug reporting
 Julien Idé -- for bug reporting
 csjacky -- for bug reporting
+Peter St. John -- for patches
 Russell Johnson -- for providing CCCBDB (NIST) logfiles
 Jerome Kieffer -- for bug reporting
+kuriba -- for patches
+Cyrille Lavigne - for documentation
 Greg Magoon -- for bug reporting and patches
+Alex Maldonado -- for fixes
 Scott McKechnie -- for bug reporting
 mkrompiec -- for contributing test files
 mwykes -- for bug reporting and patches
 Alexis Otero-Calvis -- for bug reporting
+Daniele Padula -- for patches
 Rob Paton -- for creating and running Jaguar test jobs
 Martin Peeks -- for patches
+Waylon Peng -- for fixes and improvements
+Mark Perri -- for patches
 Felix Plasser -- for fixes, patches and contributing files
 Martin Rahm -- for bug reporting
 Peter Reinholdt - for patches
@@ -50,18 +65,24 @@ Jaime Rodríguez-Guerra - for patches
 Tamilmani S -- for bug reporting
 Melchor Sanchez -- for bug reporting
 Alex Schild -- for ideas and contributing test files
-Felipe S. S. Schneider - for fixes
 Jen Schwartz -- for helping create and run Jaguar 6.0 test jobs
+shijunang -- for patches
+Chikashi Shinagawa -- for patches
+simonaxelrod -- for fixes
 Tiago Silva -- for bug reporting
+James E T Smith -- for fixes
 Pavel Solntsev -- for bug reporting
+srtlg -- for fixes
 Ben Stein -- for patches
 Maxim Stolyarchuk - for patches
 Adam Swanson -- for bug reporting
 Joe Townsend -- for contributing multiple GAMESS files to test on
-Shiv Upadhyay -- for patches and fixes
 Chengju Wang -- for bug reporting
-Andrew Warden -- for bug reporting
+Andrew Warden -- for bug reportint
+Hubert Weißmann -- for fixes
+Dustin Wheeler -- for fixes
 Samuel Wilson -- for bug reporting
+Dave Z. -- for patches
 Fedor Zhuravlev -- for patches
 
 Please let us know if we have omitted someone from this list.

cclib/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021, the cclib development team
+# Copyright (c) 2022, the cclib development team
 #
 # This file is part of cclib (http://cclib.github.io) and is distributed under
 # the terms of the BSD 3-Clause License.
@@ -25,7 +25,7 @@
 as well as example methods that take parsed data as input.
 """
 
-__version__ = "1.7.1"
+__version__ = "1.7.2"
 
 from cclib import parser
 from cclib import progress

cclib/method/ddec.py

@@ -712,7 +712,11 @@ def _converge_phi(self, phiA, superscript, atomi):
         candidates_phi = [phiA]
         candidates_bigphi = [bigphiA]
 
+        it_max = 200
+        curr_it = 0
+
         while phiA <= 0:
+            curr_it += 1
             # Iterative algorithm until convergence
             # Refer to S101 in doi: 10.1039/c6ra04656h
             if superscript == 1:
@@ -736,6 +740,10 @@ def _converge_phi(self, phiA, superscript, atomi):
             candidates_phi.append(phiA)
             candidates_bigphi.append(bigphiA)
 
+            if curr_it == it_max:
+                self.logger.info("Hit iteration max")
+                break
+
         return candidates_phi, candidates_bigphi
 
     def _parabolic_fit(self, pseudodensity, superscript, atomi):

cclib/parser/adfparser.py

@@ -166,7 +166,7 @@ def extract(self, inputfile, line):
         # this with the previous block, if possible.
         if line[:6] == "Create":
             while line[:5] != "title" and "NO TITLE" not in line:
-                line = inputfile.next()
+                line = next(inputfile)
 
         if line[1:10] == "Symmetry:":
             info = line.split()
@@ -322,17 +322,17 @@ def extract(self, inputfile, line):
 
             self.skip_line(inputfile, 'blank')
 
-            line = inputfile.next()
+            line = next(inputfile)
             while line.strip():
 
                 colline = line
                 assert colline.split()[0] == "column"
                 columns = [int(i) for i in colline.split()[1:]]
 
-                rowline = inputfile.next()
+                rowline = next(inputfile)
                 assert rowline.strip() == "row"
 
-                line = inputfile.next()
+                line = next(inputfile)
                 while line.strip():
 
                     i = int(line.split()[0])
@@ -342,9 +342,9 @@ def extract(self, inputfile, line):
                         overlaps[k-1][i-1] = o
                         overlaps[i-1][k-1] = o
 
-                    line = inputfile.next()
+                    line = next(inputfile)
 
-                line = inputfile.next()
+                line = next(inputfile)
 
             # Now all values should be parsed, and so no Nones remaining.
             assert all([all([x is not None for x in ao]) for ao in overlaps])
@@ -954,23 +954,23 @@ def extract(self, inputfile, line):
 #            # There will be some text, followed by a line:
 #            #       (power of) X  Y  Z  R     Alpha  on Atom
 #            while not line[1:11] == "(power of)":
-#                line = inputfile.next()
-#            dashes = inputfile.next()
-#            blank = inputfile.next()
-#            line = inputfile.next()
+#                line = next(inputfile)
+#            dashes = next(inputfile)
+#            blank = next(inputfile)
+#            line = next(inputfile)
 #            # There will be two blank lines when there are no more atom types.
 #            while line.strip() != "":
 #                atoms = [int(i)-1 for i in line.split()[1:]]
 #                for n in range(len(atoms)):
 #                    self.atombasis.append([])
-#                dashes = inputfile.next()
-#                line = inputfile.next()
+#                dashes = next(inputfile)
+#                line = next(inputfile)
 #                while line.strip() != "":
 #                    indices = [int(i)-1 for i in line.split()[5:]]
 #                    for i in range(len(indices)):
 #                        self.atombasis[atoms[i]].append(indices[i])
-#                    line = inputfile.next()
-#                line = inputfile.next()
+#                    line = next(inputfile)
+#                line = next(inputfile)
 
         if line[48:67] == "SFO MO coefficients":
 

cclib/parser/daltonparser.py

@@ -530,7 +530,7 @@ def extract(self, inputfile, line):
 
             self.skip_lines(inputfile, ['d', 'b'])
 
-            line = inputfile.next()
+            line = next(inputfile)
             self.symcounts = [int(c) for c in line.split(':')[1].split()]
 
             self.symlabels = []
@@ -540,7 +540,7 @@ def extract(self, inputfile, line):
 
                 # If the number of orbitals for a symmetry is zero, the printout
                 # is different (see MP2 unittest logfile for an example).
-                line = inputfile.next()
+                line = next(inputfile)
 
                 if sc == 0:
                     assert "No orbitals in symmetry" in line
@@ -549,7 +549,7 @@ def extract(self, inputfile, line):
                     self.symlabels.append(line.split()[1])
                     self.skip_line(inputfile, 'blank')
                     for i in range(sc):
-                        orbital = inputfile.next()
+                        orbital = next(inputfile)
 
         if "Starting in Wave Function Section (SIRIUS)" in line:
             self.section = "SIRIUS"

cclib/parser/data.py

@@ -75,6 +75,7 @@ class ccData:
         optstatus -- optimization status for each set of atomic coordinates (array[1])
         polarizabilities -- (dipole) polarizabilities, static or dynamic (list of arrays[2])
         pressure -- pressure used for Thermochemistry (float, atm)
+        rotconsts -- rotational constants (array[2], GHz)
         scancoords -- geometries of each scan step (array[3], angstroms)
         scanenergies -- energies of potential energy surface (list)
         scannames -- names of variables scanned (list of strings)
@@ -166,8 +167,8 @@ class ccData:
        "point_group":      Attribute(str,              'symmetry point group',        'properties:rotational'),
        "polarizabilities": Attribute(list,             'polarizabilities',            'N/A'),
        "pressure":         Attribute(float,            'pressure',                    'properties'),
-       "roconst":          Attribute(numpy.ndarray,    'rotational constants',        'properties:rotational'),
-       "rotemp":           Attribute(numpy.ndarray,    'rotational temperatures',     'properties:rotational'),
+       "rotconsts":        Attribute(numpy.ndarray,    'rotational constants',        'atoms:coords:rotconsts'),
+       "rottemp":           Attribute(numpy.ndarray,    'rotational temperatures',     'properties:rotational'),
        "s2_after_anni":    Attribute(numpy.ndarray,    'S2 after annihilation',       'optimization'),      
        "s2_after_anni_fin": Attribute(float,           'S2 after annihilation',       'properties'),      
        "s2_before_anni":   Attribute(numpy.ndarray,    'S2 before annihilation',      'optimization'),      

cclib/parser/gamessukparser.py

@@ -721,13 +721,13 @@ def extract(self, inputfile, line):
             occupations = []
 
             self.skip_line(inputfile, "blank")
-            line = inputfile.next()
+            line = next(inputfile)
 
             while line.strip():
                 occupations += map(float, line.split())
 
                 self.skip_line(inputfile, "blank")
-                line = inputfile.next()
+                line = next(inputfile)
 
             self.set_attribute('nooccnos', occupations)