Resolve "Enabling free Maxwell propagation in multisystem mode, part 2/4"

added 210 commits

35b97d62 - defining exchange energy
83b59b8d - scf.f90 file: fixing restart, adding output of correlator, pt_number, pt_exchange, ss
ef3117d1 - update Makefile.am to deal with new files photon_mode.F90 and xc_oep_qed_inc.F90
870990f0 - adding pt_exchange to energy_calc.F90
04cdbbbb - adding pt_exchange to ks%calc_energy
78f217fc - photon kli by Christian Schaefer (christian.schaefer@mpsd.mpg.de)
052754c6 - photon oep
5bcaac41 - photon oep _inc file
fa801020 - two new files, photon mode and xc_oep_qed_inc.F90
dc716e01 - bugix
adb5da25 - adding correct output of normss
b21afa32 - adding line break for cuda/mpi compiler
0c4f30a5 - comment with reference to photon oep paper on arxiv
0d41cd74 - adding experimental warning if photons=yes
3d10dfc6 - Merge branch 'photon-oep' into 'master'
76b77030 - Merge branch 'master' into 'photon-oep'
614b5f92 - resolving two problems due to merge with master branch (v8.2)
ce332a1e - Merge branch 'photon-oep' into 'photon-oep'
a7145076 - Replace Makefile.am by Christian Schaefer
00fe9134 - Revert "Replace Makefile.am by Christian Schaefer"
57156522 - Merge branch 'revert-a7145076' into 'photon-oep'
f39446a6 - changed oep to many photon mode syntax
efd2a538 - removing comments
f79322f4 - updating the photonmode file
e2802f40 - fixing problems for spinresolved calculations
8d4bf07f - Merge branch 'develop' into HEAD
bad9242d - using nst
9b707c9f - oep should only run over occupied states
eb27abc4 - adding a line that has been removed unintentionally
0b2aad69 - integer need to be declared
28d26828 - spin unrestricted OEP should work now, we need some proper tests
d9dd8c0a - spin-resolved related changes
0282905d - fixing the output of the photon_correlator
1ec557a3 - Merge branch 'develop' into 'photon-oep'
8f934696 - removing comments that were not up to date
be143cc4 - changing order of deallocation, photonmode has only to be called if run with photons
b5bfd3a0 - Merge branch 'develop' into 'photon-oep'
c190a81c - fixing the intent argument for KLI routine
3cf80565 - Included center-of-charge shift for the dipole operator into the photon
dc659f12 - Included KLIpt_coc parameter (default=false) to enable switching between
00c76a19 - Merge branch 'develop' into HEAD
3c1a09bf - fixing the errors of the testsuite, now everything should run through
377db06c - Merge branch 'photon-oep' into 'develop'
6a79d4d4 - Merge branch 'develop' into 'photon-oep'
6b18189a - include break-line in coc-shift to avoid Fortran maxcharacter issue
9e191c0a - fixing the cuda mpi error by explicitely specifying dimensions
aa38ac74 - fix reference and only allow spin-unpolarized (for now)
95b324c6 - using axpy for increased performance
af98324b - Adding the support for complex-to-complex ffts.
6197b3f3 - Merge branch 'develop' into complex_fft
73012ec6 - The complex FFT caanot be used with dressed Poisson solver.
18dde712 - If we want to do complex-to-complex FFTs, we need to have memory allocated to the proper size.
efc8bac6 - The two-body integrals and related exchange integrals are now computed using a...
a04bcff8 - Merge branch 'develop' into photon-oep
6fd314ce - adding the namespace variable for the linear solver
f4060f64 - adding a testfile for photon OEP and KLI
4e6a1dcc - changing output pt_exchange/number -> photon exchange/number
d3b96e9e - adding the test input files
17366213 - Explicitly specify dimension
f3a8abf8 - also print photon energy and number for KLI
a2f626e4 - Adding message not implemented for Slater approximation and one fixing typo.
51c21439 - Some small fixes related to coding standards.
e5eb9049 - It is now possible to run HF and hybrid calculations for solids for an...
f0500041 - Merge branch 'develop' of gitlab.com:octopus-code/octopus into develop
087581f4 - In case FFT kernel is real, we cannot use the complex-to-complex routine from zpoisson_fft_solve.
efb49332 - Fix a warning.
fb61e929 - Fix the behavior for the calculation of the Coulomb singularity in...
d8238bee - Fix the use of singularity for screened hybrids in isolated systems.
0a506208 - first set of cleaning of code as suggested by Micael
ba1369c7 - fixing loop
3ac35680 - changes to comply with coding standards
62fae345 - coding standard, cleaning photon mode module, moving lr to oep module, using dotu in mf_dotp
9d22f3da - Merge branch 'develop' into photon-oep
80e9659f - Merge branch 'develop' into photon-oep
a98b5d53 - Fix a problem with the input variable FFTPreparePlan, which was not working.
fc8c2de9 - Fix merge conflict with develop.
7e727119 - Merging with develop.
9c87b457 - Proper comparison of logicals.
1d6fbc4c - Fix a left over from merge conflict.
0f4d6dc4 - Proper comparison of logicals.
0e6227f8 - Add a missing change for ISF.
759d1056 - The exhange operator is only initialized when needed.
295220a1 - RDMFT also need the exchange operator.
016106aa - We also need it for the OEP.
cfea1133 - Several improvements to the linked lists and how the systems are handled.
6e707143 - Merge branch 'improve_system_linked_list' into 'develop'
9896aeba - First step towards implemented a new logic for propagators and multisystems.
35065f31 - Adding a demonstrator based on celestial_bodies. Not working yet.
bf45823b - Making the celestial dynamics more complete, with a implementation of the...
7e5c7065 - Small changes to make the celestial dynamics produce a meaningful result.
98b2b4e3 - Celestial body's properties are now parsed from the input file.
bb36e0d3 - Add a namespace to the abstract system, as all systems should have their own namespace.
969e7d16 - Improve class arguments naming scheme consistency. Minor cosmetic changes.
2dd4d59d - Make sure forces are initialized to zero.
d2ebb002 - No need to have a init deferred method for propagators.
fa5f72de - The propagator verlet is now initialized with a function that overloads the type.
29d62250 - Move the calculation of the force between two celestial bodies to a new...
7a7aa5db - Make propagator_finished a method of the abstract propagator. Now only...
dc6c2de7 - Print some debug information when running a propagation step.
d6c829d0 - Nicer output during the celestial dynamics test mode. Systems are now required...
6ed63fa3 - Actually stop the propagation once we are finished!
1c584981 - Add routines to finalize celestial body.
ff3dc7eb - celestial_body_init is not a class method anymore. Instead, it is now a...
54325e8b - The multisystem framework is now aware of the existence of celestial bodies.
3f762d04 - Collapse two if statements.
5af35405 - Merge branch 'photon-oep' into 'develop'
129e256f - Major refactoring of the new framework for propagators and interactions.
05fe5fa3 - Add new CelestialDynamics.html file to Makefile.
95506db6 - New methods for the celestial body class to write information during the td run.
5bdaccad - Add units of the celestial body's input options.
521aeede - Make the propagator a component of the abstract system.
23e47c80 - Update celestial dynamics test.
752db736 - Moved the known propagator operations to propagator_abst_oct_m.
0a282852 - Renamed system_dt to system_dt_operation and the corresponding class method to dt_operation.
61c9e06e - Move the set_propagator method to the abstract system.
6121b197 - Update celestial dynamics test reference values and tolerances.
b07514d5 - Merge branch 'toward_multisystem_propagators' into 'develop'
9f8e4af4 - Add a missing initialization.
934f033f - Fix a bug with dim<3 and cell angles.
75a142f3 - Combining the routines zpoisson_solve_fft and dpoisson_solve_fft to avoid code duplications.
82401438 - Fix bug: wrong arrays were passed
c44cb917 - Refactor allocation code and fix memory leak for deallocation
c6cbfe42 - Remove gpg output for the git revision that is baked into the octopus binary.
682e309b - This value should always be initialized.
1f764cf1 - Adding first very simple simulation clock implementation
49b2c7bd - Add granularity to the clock to be able to compare clocks globally.
5b026b3a - Add number of algorithmic steps to the abstract propagator
f0797dd3 - Rename routines for clock comparison.
1463f979 - Add function to decrement clock by one tick.
01a7d278 - Adding function is_later_with_step to clock.
43694eeb - Overload operators for clock.
b89b4dd8 - Add print function
a2947f71 - Update overloaded operator definition and epoch timers
1886d97b - Add namespace to clock and improve output format of clock print function
f465ed1e - Add unit test for clock
71533e3c - Switch from boolean to integer output values for the testsuite
aad1e0df - Add regression test for clock
3fb17432 - Add finest system wide tick to clock print function
3f16abbf - Add more print statements to clock unit test
b652cf86 - Break long lines for the gfortran configuration in the buildbot
615b80d0 - Remove unused variables
46c14fd3 - Revert to test_celestial_dynamics routine from develop
0b1bbb07 - Merge branch 'complex_fft' into 'develop'
26916603 - Merging with develop. This does not compile for the moment.
16ac056d - Merge branch '276-Add-support-for-gpg-signatures-in-git-commits' into 'develop'
d6619f33 - Merge branch 'improved_fftw_support' into 'develop'
4246000f - Merge branch 'fix_cell_angle_low_dim' into 'develop'
d4d507e1 - Addressing issues raised in the code review
9597252a - Further updates based on the code review for the MR
c9c1b874 - Allow to increment or decrement the clock ticks by more than one step
65a0579d - Rename simulation_clock to clock
ed6be314 - Remove epoch variables from clock
3e2e81c0 - modules and variables renamed to psolver_
73f839ae - Add documentation for the clock
81938a0f - reverted to HAVE_LIBIFS to avoid breaking the tests for other branches
17cbaa1b - Merge branch '273-add-simulation-clocks-for-multi-system-synchronization-v2' into 'develop'
033cafb9 - Make batched current default for non-orthogonal cells
db0b7650 - Remove unnecessary application of the phase to the gradient.
56c3efd3 - resolve style issues
f011386d - Fix a memory leak in the current calculation in GPU.
9dd277c6 - Adding an assert to check the assumption used in the code.
f0ea83f6 - Split the set function of the clock to a full set, including namespace and a time set only
688aa79e - Adding clock print_str and print_message functions
1efd8bdd - Merge branch '278-rename-poisson_libisf_oct-to-poisson_psolver_oct' into 'develop'
aaf12cb7 - Align intents and remove one trim
a9c2efb3 - Rename clock_set_all to clock_copy
9cdd1cdd - The kernel of the FFT is now isolated from the Poisson solver itself. This...
b1479646 - Fix some problems with the previous commit and adjust a test, as the code was...
c2479926 - Merge branch 'current_batch_gradient' into 'develop'
34ba4a64 - Only compile Libyaml if LibISF was not found.
4cef4fa6 - Add check for latest version of PSolver.
30330c57 - PSolver support updated to allow for new and old API's. New API adds support...
ae25c505 - Renamed libisf to psolver in several places (documentation, variables, tests, etc)
75382e44 - Mark use of olver versions of PSOlver as deprecated.
aadcbf64 - Rename poisson_libisf.F90 to poisson_psolver.F90.
4f65635d - warning fixed (hartree_energy)
39cc4cfe - Merge branch '279-update-poisson_psolver_oct-to-allow-for-both-the-old-and-new-api' into 'develop'
3babc8b7 - Simplifies the logic of the code.
eb012bb3 - Remove unused first method and generic add method from linked list.
ec587d80 - Add linked list method to iterate
77db56aa - Rename functions in linked list module to make them less generic and closer to...
e493c6ed - Remove namespace from clock
70d50756 - Remove print_message function from clock
1e03e53d - added explicit specification of MPI group for the Psolver
864c8766 - Merge branch 'develop' into exchange_for_solids
e216954e - Use new linked list iterate method to simplify some loops.
875eca83 - Merge branch 'develop' into 280-improved-clock-printing-and-setting
4ea5a651 - Since the propagator is a list of instruction, we make it an extension of a linked list.
51b48311 - Removed iterator from linked list.
0369ff53 - Add wrapper class for list of interactions.
128c9bac - Adding a nullify routine to avoid problem in releasing memory hat was not allocated.
f7a50bb7 - For some strange reason this value got modified in the commit...
38dbcd3d - Use messages_fatal instead of output to stderr
1d954d96 - Add a list_counter class that implements the necessary methods to iterate over...
d28dc311 - The propagator now uses the list counter.
6ffa8fc3 - Renamed counter_end_of_list to counter_has_next.
ceeaf75a - Add missing push/pop
e85f44cb - Transform the list counter into a proper iterator.
75233c5f - enabled PSOLVER for serial builds
d2e3b22d - Merge branch 'more_lists' into 'develop'
2045947a - The range of the soft Coulomb potential is now set by according to...
c9b1fb66 - Merge branch '280-improved-clock-printing-and-setting' into 'develop'
a3d54419 - Merge branch 'soft_coulomb_threshold' into 'develop'
cf5ea6ea - The clock-related operator and the assignment are now methods of the class....
f1f76808 - added some comments
7f188017 - Merge branch 'clock_class_operators' into 'develop'
17338809 - Merge branch 'exchange_for_solids' into 'develop'
58eb303d - Merge branch '282-enable-psolver-for-sequential-runs' into 'develop'
e18a00c0 - Fix a problem with array dimensions.
39263646 - Merging with develop and fixing the conflicts.

Codecov Report

Merging #784 into develop will increase coverage by 1.51%. The diff coverage is 54.34%.

@@             Coverage Diff             @@
##           develop     #784      +/-   ##
===========================================
+ Coverage    69.26%   70.78%   +1.51%     
===========================================
  Files          505      500       -5     
  Lines        98106    97621     -485     
===========================================
+ Hits         67958    69104    +1146     
+ Misses       30148    28517    -1631

Impacted Files	Coverage Δ
src/grid/mesh.F90	`70.25% <ø> (-1.86%)`
src/grid/restart.F90	`89.00% <ø> (-2.49%)`
src/hamiltonian/hamiltonian_mxll.F90	`21.64% <ø> (+2.49%)`
src/math/maxwell_function.F90	`25.42% <ø> (-0.28%)`
src/states/states_mxll.F90	`51.44% <ø> (-7.31%)`
src/system/system_abst.F90	`67.85% <ø> (-4.40%)`
src/td/propagator_base.F90	`0.00% <ø> (ø)`
src/td/propagator_mxll.F90	`31.95% <ø> (+10.87%)`
src/td/td.F90	`75.07% <ø> (+0.40%)`
src/td/td_write.F90	`58.18% <ø> (-0.21%)`
... and 272 more

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added 1 commit

b456d9b3 - Add a missing allocation of the pointer inside the system_mxll_init routine.

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added 3 commits

86e98f0a - The maxwell systems where not added to the system list.
8718f7d7 - This variable was not initialised.
c392a77b - Add explicit sizes for array copies.

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added 634 commits

c392a77b...32bd0e92 - 634 commits from branch 205-enabling-free-maxwell-propagation-in-multisystem-mode-part-1-4

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changed the description

changed target branch from 205-enabling-free-maxwell-propagation-in-multisystem-mode-part-1-4 to develop

added 8 commits

32bd0e92...ef1b008a - 5 commits from branch develop
f5c39894 - Add necessary calls inside mxll_propagation_step and transform_rs_densities...
f29ad512 - Add external current test files, still doesn't match with previous tests but numbers are similar
e65c50e5 - Add message_fatal for Maxwell-matter coupling

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assigned to @fbonafe

assigned to @heiko.appel and unassigned @fbonafe

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2bfc2e75 - Fix calls in mxll_propagation_step and get_rs_density_ext and update test...

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changed milestone to %11.0

added 2 commits

7be31d01 - Fix implementation of inhomogeneity propagation with no approximation which...
8ad8d1b0 - Attempt to solve valgrind problems arising from unitilized values, probably in...

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added 1 commit

ac28f850 - Solve valgrind issues

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added 1 commit

8fc867b0 - Change external current pointers to allocatables in states_mxll

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unmarked as a Work In Progress

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Resolve "Enabling free Maxwell propagation in multisystem mode, part 2/4"

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Resolve "Enabling free Maxwell propagation in multisystem mode, part 2/4"

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