Merge branch 'develop'
Merge branch 'develop'
Merge branch 'develop'
Started building the QM/MM Hybrid capabilities to pysic.
Made a new class for handling hybrid calculations. Also added a class
for representing the different embedding schemes.
Hybrid calculations are performed by using "hybridcalculation.py".
This leaves the calculator.py unchanged (preventing me from breaking it)
Added the calculation of electrostatic interaction between subsystems.
Added test scripts for debugging and validating the code. Modified the
warn()-function a bit. Fixed stuff.
Slight modifications to test systems
Fixed a problem with interactions between link atoms. Added a new
"SubSystem" class.
Added initial support for external calculators, such as GPAW.
Also added a test script for testing GPAW calculations.
Added an interface to AtomEye3 for easy test visualization. Also created
a water system for test purposes.
-Added a python interface to AtomEye (under utilities)
-Added a few classes for storing subsystem/binding information in separate files
-Dynamics are now supported
Added support for dynamics, added dynamic charge calculation from pseudo
density, added new test cases, added color coding for subsystems in AtomEye
visualization
Added a test case for running GPAW with MPI parallellization, changed
the interface, added sript or making solution
Corrected the link atom correction calculation, enabled force
calculation for periodic systems, accurate time statistics, et.
All sort of things added, better MPI-support, Bader charge calculation,
better documentation.
Added better documentation, enabled multiple types of hydrogen links
(=with different CHL parameters), time recording is now on by default
Separated the bader charge analysis to a separate file under the utitlity
folder. Removed the test files from git.
Fixed issues with some sphinx markup, removed more test files