Merge pull request #22 from langner/master

Updates for v1.5

Author: langner

_sources/attributes.txt

@@ -30,6 +30,7 @@
     `grads`_            current values of forces (gradients) in geometry optimization                                array of rank 3
     `hessian`_          elements of the force constant matrix                                                        array of rank 1
     `homos`_            molecular orbital indices of HOMO(s)                                                         array of rank 1
+    `metadata`_         various metadata about the package and computation                                           dict
     `mocoeffs`_         molecular orbital coefficients                                                               list of arrays of rank 2
     `moenergies`_       molecular orbital energies                                       eV                          list of arrays of rank 1
     `moments`_          molecular multipole moments                                      a.u.                        list of arrays[]
@@ -43,6 +44,7 @@
     `nooccnos`_         natural orbital occupation numbers                                                           array of rank 1
     `optdone`_          flags whether an optimization has converged                                                  Boolean
     `optstatus`_        optimization status for each set of atomic coordinates                                       array of rank 1
+    `polarizabilities`_ (dipole) polarizabilities, static or dynamic                                                 list of arrays of rank 2
     `scancoords`_       geometries of each scan step                                     angstroms                   array of rank 3
     `scanenergies`_     energies of potential energy surface                                                         list
     `scannames`_        names of varaibles scanned                                                                   list of strings
@@ -51,6 +53,7 @@
     `scftargets`_       targets for convergence of the SCF                                                           array of rank 2
     `scfvalues`_        current values for convergence of the SCF                                                    list of arrays of rank 2
     `temperature`_      temperature used for Thermochemistry                             kelvin                      float
+    `time`_             time in molecular dynamics and other trajectories                fs                          array of rank 1
     `vibanharms`_       vibrational anharmonicity constants                              1/cm                        array of rank 2
     `vibdisps`_         cartesian displacement vectors                                   delta angstrom              array of rank 3
     `vibfreqs`_         vibrational frequencies                                          1/cm                        array of rank 1
@@ -88,6 +91,7 @@
 .. _`grads`: data_notes.html#grads
 .. _`hessian`: data_notes.html#hessian
 .. _`homos`: data_notes.html#homos
+.. _`metadata`: data_notes.html#metadata
 .. _`mocoeffs`: data_notes.html#mocoeffs
 .. _`moenergies`: data_notes.html#moenergies
 .. _`moments`: data_notes.html#moments
@@ -101,6 +105,7 @@
 .. _`nooccnos`: data_notes.html#nooccnos
 .. _`optdone`: data_notes.html#optdone
 .. _`optstatus`: data_notes.html#optstatus
+.. _`polarizabilities`: data_notes.html#polarizabilities
 .. _`scancoords`: data_notes.html#scancoords
 .. _`scanenergies`: data_notes.html#scanenergies
 .. _`scannames`: data_notes.html#scannames
@@ -109,6 +114,7 @@
 .. _`scftargets`: data_notes.html#scftargets
 .. _`scfvalues`: data_notes.html#scfvalues
 .. _`temperature`: data_notes.html#temperature
+.. _`time`: data_notes.html#time
 .. _`vibanharms`: data_notes.html#vibanharms
 .. _`vibdisps`: data_notes.html#vibdisps
 .. _`vibfreqs`: data_notes.html#vibfreqs

_sources/attributes_dev.txt

@@ -30,6 +30,7 @@
     `grads`_            current values of forces (gradients) in geometry optimization                                array of rank 3
     `hessian`_          elements of the force constant matrix                                                        array of rank 1
     `homos`_            molecular orbital indices of HOMO(s)                                                         array of rank 1
+    `metadata`_         various metadata about the package and computation                                           dict
     `mocoeffs`_         molecular orbital coefficients                                                               list of arrays of rank 2
     `moenergies`_       molecular orbital energies                                       eV                          list of arrays of rank 1
     `moments`_          molecular multipole moments                                      a.u.                        list of arrays[]
@@ -43,6 +44,7 @@
     `nooccnos`_         natural orbital occupation numbers                                                           array of rank 1
     `optdone`_          flags whether an optimization has converged                                                  Boolean
     `optstatus`_        optimization status for each set of atomic coordinates                                       array of rank 1
+    `polarizabilities`_ (dipole) polarizabilities, static or dynamic                                                 list of arrays of rank 2
     `scancoords`_       geometries of each scan step                                     angstroms                   array of rank 3
     `scanenergies`_     energies of potential energy surface                                                         list
     `scannames`_        names of varaibles scanned                                                                   list of strings
@@ -51,6 +53,7 @@
     `scftargets`_       targets for convergence of the SCF                                                           array of rank 2
     `scfvalues`_        current values for convergence of the SCF                                                    list of arrays of rank 2
     `temperature`_      temperature used for Thermochemistry                             kelvin                      float
+    `time`_             time in molecular dynamics and other trajectories                fs                          array of rank 1
     `vibanharms`_       vibrational anharmonicity constants                              1/cm                        array of rank 2
     `vibdisps`_         cartesian displacement vectors                                   delta angstrom              array of rank 3
     `vibfreqs`_         vibrational frequencies                                          1/cm                        array of rank 1
@@ -88,6 +91,7 @@
 .. _`grads`: data_notes.html#grads
 .. _`hessian`: data_notes.html#hessian
 .. _`homos`: data_notes.html#homos
+.. _`metadata`: data_notes.html#metadata
 .. _`mocoeffs`: data_notes.html#mocoeffs
 .. _`moenergies`: data_notes.html#moenergies
 .. _`moments`: data_notes.html#moments
@@ -101,6 +105,7 @@
 .. _`nooccnos`: data_notes.html#nooccnos
 .. _`optdone`: data_notes.html#optdone
 .. _`optstatus`: data_notes.html#optstatus
+.. _`polarizabilities`: data_notes.html#polarizabilities
 .. _`scancoords`: data_notes.html#scancoords
 .. _`scanenergies`: data_notes.html#scanenergies
 .. _`scannames`: data_notes.html#scannames
@@ -109,6 +114,7 @@
 .. _`scftargets`: data_notes.html#scftargets
 .. _`scfvalues`: data_notes.html#scfvalues
 .. _`temperature`: data_notes.html#temperature
+.. _`time`: data_notes.html#time
 .. _`vibanharms`: data_notes.html#vibanharms
 .. _`vibdisps`: data_notes.html#vibdisps
 .. _`vibfreqs`: data_notes.html#vibfreqs

_sources/changelog.txt

@@ -4,10 +4,44 @@
 Changelog
 =========
 
-Changes since cclib-1.3.2
--------------------------
+Changes in cclib-1.5
+--------------------
 
-**Feaures**
+**Features**
+
+* Support for both reading and writing CJSON (Sanjeed Schamnad)
+* New parser: cclib can now parse MOPAC files (Geoff Hutchison)
+* New attribute time tracks coordinated for dynamics jobs (Ramon Crehuet)
+* New attribute metadata holds miscellaneous information not in other attributes (bwang2453)
+* Extract moments attribute for Gaussian (Geoff Hutchison)
+* Extract atombasis for ADF in simple cases (Felix Plaser)
+* License change to BSD 3-Clause License
+
+**Bugfixes**
+
+* Correct parsing of several attributes for ROHF calculations
+* Fixed precision of scfvalues in ORCA
+* Fixed MO parsing from older versions of Firefly (mkrompiec)
+
+Changes in cclib-1.4.1
+----------------------
+
+**Features**
+
+* Preliminary support for writing CJSON (Sanjeed Schamnad)
+* Tentative support for BOMD trajectories in Gaussian (Ramon Crehuet)
+* Support for atombasis in ADF (Felix Plasser)
+* Support for nocoeffs and nooccnos in Molpro
+
+**Bugfixes**
+
+* Fix for non-standard basis sets in DALTON
+* Fix for non-standard MO coefficient printin in GAMESS
+
+Changes in cclib-1.4
+--------------------
+
+**Features**
 
 * New parser: cclib can now parse DALTON files 
 * New parser: cclib can now parse ORCA files
@@ -33,8 +67,8 @@ Changes since cclib-1.3.2
 * Fix parsing egenvectors in GAMESS-US (Alexis Otero-Calvis)
 * Fix duplicate parsing of symmetry labels for Gaussian (Martin Peeks)
 
-Changes since cclib-1.3.1
--------------------------
+Changes in cclib-1.3.2
+----------------------
 
 **Features**
 
@@ -50,8 +84,8 @@ Changes since cclib-1.3.1
 * Fix parsing TDDFT/RPA transitions (Felix Plasser)
 * Fix encoding issues for UTF-8 symbols in parsers and bridges
 
-Changes since cclib-1.3
------------------------
+Changes in cclib-1.3.1
+----------------------
 
 **Features**
 
@@ -67,8 +101,8 @@ Changes since cclib-1.3
 * Fix parsing TDDFT/RPA transitions (Felix Plasser)
 * Fix encoding issues for UTF-8 symbols in parsers and bridges
 
-Changes since cclib-1.2
------------------------
+Changes in cclib-1.3
+--------------------
 
 **Features**
 
@@ -90,8 +124,8 @@ Changes since cclib-1.2
 * Fix parsing of Gaussian jobs with fragments and ONIOM output
 * Use UTF-8 encodings for files that need them (Matt Ernst)
 
-Changes since cclib-1.1
------------------------
+Changes in cclib-1.2
+--------------------
 
 **Features**
 
@@ -113,8 +147,8 @@ Changes since cclib-1.1
 * Handle ORCA file with AM1 output (Julien Idé)
 * Handle GAMESS-US output with irregular frequency format (Andrew Warden)
 
-Changes since cclib-1.0.1
--------------------------
+Changes in cclib-1.1
+--------------------
 
 **Feaures**
 
@@ -141,8 +175,8 @@ Changes since cclib-1.0.1
 * Apply patch from Chengju Wang to handle GAMESS calculations with more than 99 atoms
 * Handle Gaussian files with more than 99 atoms having pseudopotentials (Björn Baumeier)
 
-Changes since cclib-1.0
------------------------
+Changes in cclib-1.0.1
+----------------------
 
 **Feaures**
 
@@ -159,8 +193,8 @@ Changes since cclib-1.0
 * Handle parsing Firefly calculations that fail
 * Fix parsing of ORCA calculation (Marius Retegan)
 
-Changes since cclib-0.9
------------------------
+Changes in cclib-1.0
+--------------------
 
 **Feaures**
 
@@ -174,8 +208,8 @@ Changes since cclib-0.9
 
 * Many many additional files parsed thanks to bugs reported by users
 
-Changes since cclib-0.8
------------------------
+Changes in cclib-0.9
+--------------------
 
 **Feaures**
 
@@ -188,8 +222,8 @@ Changes since cclib-0.8
 
 * A small number of parsing errors were fixed
 
-Changes since cclib-0.7
------------------------
+Changes in cclib-0.8
+--------------------
 
 **Feaures**
 
@@ -212,8 +246,8 @@ Changes since cclib-0.7
 * Several parsing errors were fixed
 * Fixed some methods to work with different numbers of alpha and beta MO coefficients in mocoeffs (MPA, CSPA, OPA)
 
-Changes since cclib-0.6.1
--------------------------
+Changes in cclib-0.7
+--------------------
 
 **Feaures**
 
@@ -241,16 +275,16 @@ Changes since cclib-0.6.1
     - Rotations and translations now not included in frequencies
 * bridge to OpenBabel: No longer dependent on pyopenbabel
 
-Changes since cclib-0.6.0
--------------------------
+Changes in cclib-0.6.1
+----------------------
 
 **Bugfixes**
 
 * cclib: The "import cclib.parsers" statement failed due to references to Molpro and Jaguar parsers which are not present
 * Gaussian parser: Failed to parse single point calculations where the input coords are a z-matrix, and symmetry is turned off.
 
-Changes since cclib-0.6b
-------------------------
+Changes in cclib-0.6.0
+----------------------
 
 **Feaures**
 
@@ -262,8 +296,8 @@ Changes since cclib-0.6b
 * Gaussian parser: The following bugs have been fixed Parser failed if standard orientation not found
 * ccget: aooverlaps not included when using --list option
 
-Changes since cclib-0.5
------------------------
+Changes in cclib-0.6b
+---------------------
 
 **Feaures**
 
@@ -286,8 +320,8 @@ Changes since cclib-0.5
     - SCF values was not extracting the dEnergy value
     - Was extracting Depolar P instead of Raman activity
 
-Changes since cclib-0.5b
-------------------------
+Changes in cclib-0.5
+--------------------
 
 **Features**