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Author SHA1 Message Date
François Coppens
133558d98f
Merge pull request #11 from fmgjcoppens/tests 
Added environment variables source script. Added test script that loo…
 2021-02-28 09:33:39 +01:00
François Coppens
f5a2e635cf Added environment variables source script. Added test script that loops over update cycles. Added test program that loops internally over test cycles. 2021-02-28 09:28:42 +01:00
François Coppens
ba0c0c3213
Merge pull request #10 from fmgjcoppens/restructure 
Restructuring of file tree
 2021-02-27 12:29:06 +01:00
François Coppens
8e0aef7717 Restructuring complete. Updated makefile. 2021-02-27 12:25:55 +01:00
François Coppens
5d4a7af01a File tree restructured. Written build script build.sh. TODO: convert buld script into Makefile. 2021-02-26 17:28:52 +01:00
François Coppens
00fcaf2309 Replaced dataset. 2021-02-25 13:00:17 +01:00
François Coppens
a5e8ab82e9
Merge pull request #9 from fmgjcoppens/fix/cpp_interface 
Fix/cpp interface
 2021-02-25 12:40:38 +01:00
François Coppens
3df8d33bfa Problems with MaponiA3 when calling from C++ with HDF5 datasets is fixed. Bug was caused by uninitialised values of NEWed variables at several places. There are still a few remaining memory leaks. Explore with: 
valgrind --track-origins=yes --leak-check=full --show-leak-kinds=all
 2021-02-25 12:17:45 +01:00
François Coppens
225c841a88 * Fixed the 3x3 MaponiA3 C++ example. Update_index vector cannot have values that are smaller than 1 because the first colums in Fortran is stored at 1 and not 0. 
* Started debugging reading from HDF5 formatted datasets. Slater_inv needs to be transposed before sent to Maponi. Algo fails at the last step. Correct Slater and Inverse fail to produce the identity matrix. Suspect that the matMul function is not working correctly eventhough it looks like it does.
 2021-02-24 18:41:48 +01:00
François Coppens
28f6de48ee TO BE AMENDED 2021-02-23 08:28:09 +01:00
François Coppens
7f4483f19e - Made test.cpp use variable dataset. 
- Started cleanup and restructuring file tree.
 2021-02-23 07:04:55 +01:00
François Coppens
2fc4c259dc
Merge pull request #8 from fmgjcoppens/dataset 
Merge pull request #8 from fmgjcoppens/dataset
 2021-02-22 15:56:23 +01:00
François Coppens
386f29ffa9 Slightly cleaner 2021-02-22 15:53:23 +01:00
François Coppens
c29276cb7a Added tests/test to distclean in Makefile 2021-02-22 15:45:18 +01:00
François Coppens
b4787e6803 Test infrastructure for hdf5 datasets and python hdf5 datasert conversion tool. 
Made small corrections to compensate for changes made after branching-off from test_dataset.

Everything compilers
Everything works except for the HDF5 dataset test program that gives an I/O error.
 2021-02-22 15:44:41 +01:00
François Coppens
b2b4756b53 Problem solved. Problems was caused by reading the inverse matrix S_inv the same way as the matrix S, but apparently what has been stored is transpose(S_inv) and not S_inv. Therefore it needs to be read transposed compared to S in order to for S*S_inv to give the Identity matrix. 
TODO: Calls from C/C++ are still broken because inside the MaponiA3 algo there is compensation for the fact that Fortran sends it's arrays in column-major order. This must be resolved by  transposeing S_inv before it is passed to MaponiA3 and remove the compensations made there.
 2021-02-22 15:43:27 +01:00
François Coppens
8d63dd1701 The algorithm now works for the following 4x4 example with 2 updates: 
S = [1,0,1,-1; 0,1,1,0; -1,0,-1,0; 1,1,1,1]
S_inv = [1,-1,1,1; 1,0,2,1; -1,1,-2,-1; -1,0,-1,0]
u1 = [0,-2,0,0]
u2 = [0,-1,0,0]
upd_idx = [2,4]

To go from Maponi's examples where the number of updates is always equal
to the the dimension of the matrix, and the decomposition is always
diagonal, to cases with a non-diagonal decomposition and a number of
updates unequal to its size, the following changed needed to be made:

* in the calculation of the {y0k} an extra inner for-loop needs to be
  added to make it a full matrix-vector multiplication due to the fact
  that A0 is not a diagonal matrix

* in some places the use of the update-order vector p needs
  the be replaced with that of upd_idx to make sure the correct
  component of the ylk is selected and the proper rank-1 matrices are
  constructed

* when a matrix is passed from Fortran to C++ with 2D adressing, it is
  passed in colum-major order. The passed matrix needs to be transposed
  before passing to C++. Doing this inside the algorithm will break
  compatibility with called from C/C++.
 2021-02-22 15:41:30 +01:00
François Coppens
5b56a8e8a7 Debugging in progress... 2021-02-22 15:38:39 +01:00
François
48c27eb47e * Modified Maponi algo 3 so that it can be used with a number of updates 
that is smaller than the size of the Slater-matrix
* Removed the Slater-matrix as an argument, since it is not used in the
  algo.
* Added a manual 4x4 example to debug MaponiA3 to work with a number of
  updates that is smaller than the size of the Slater-matrix
* Added a new Octave script to quickly check if the computes inverse is
  correct.
 2021-02-22 15:34:34 +01:00
François Coppens
f17a7a2c9b
Merge pull request #6 from pablooliveira/test-datasets 
Test datasets
 2021-02-16 15:06:04 +01:00
Pablo Oliveira
061c9b9f21 Add test infrastructure for datasets 2021-02-16 10:49:15 +01:00
François Coppens
90469df3c2 Put importing the dataset into a module. 2021-02-12 19:31:31 +01:00
François Coppens
6b699143b5 Added some test output in the Fortran prgram to load into Octave for quick checking. 2021-02-12 17:48:49 +01:00
François Coppens
1b3a1d9d22 Added QMCChem test dataset with 3 updates. Renamed files, added the Fortran program QMCChem_dataset_test.f90 to start testing the QMCChem dataset. Wrote and tested Fortran code to import the test dataset. 2021-02-12 12:04:21 +01:00
François Coppens
1983b7883f
Merge pull request #5 from pablooliveira/flatten 
C++ redesign of data-structures
 2021-02-09 17:03:56 +01:00
Pablo Oliveira
da41c57ee2 No need to zero out breakdown vector 2021-02-09 15:09:37 +01:00
Pablo Oliveira
2d2085f739 Simplify initialization with 0 2021-02-09 15:07:55 +01:00
Pablo Oliveira
b9efd7ef0b Optimize out the U 2021-02-09 15:05:11 +01:00
Pablo Oliveira
aa78f94177 Apply clang-format 2021-02-09 14:46:28 +01:00
Pablo Oliveira
b575cda8d6 Optimize out Identity matrix 2021-02-09 14:44:54 +01:00
Pablo Oliveira
6f34f485d3 C++ redesign of data-structures 
- Use flat arrays
- Use real type for all matrices
- Merge _f MaponiA3 files
 2021-02-09 14:34:39 +01:00
François Coppens
de00fbadff
Merge pull request #4 from fmgjcoppens/feature/c-from-fort 
Calling C++ function MaponiA3 from Fortran
 2021-02-08 11:24:19 +01:00
François Coppens
b0140cbc07 Changed some comments. 2021-02-06 19:11:02 +01:00
François Coppens
3f6bca2b04 The Fortran interface to C++ fuction MaponiA3() works but the mechanism of passing the 2D arrays from Fortran to C++ must be improved. Now the passed 'linear' 2D arrays are copied and reshaped into usable 2D arrays. This needs to be replaced with some suitable casting mechanism. 2021-02-06 18:59:07 +01:00
François Coppens
7f7b23f7c4 Put more comments in Makefile. 2021-02-04 18:52:26 +01:00
François Coppens
f1641dd4e4 Solved linking problem by including C++ standard library '-lstdc++'. Also added a minimal working example of Fortran-C++ interfacing in dir 'mwe'. 2021-02-04 17:05:55 +01:00
François Coppens
84fffdb7fa Prepared the example matrix of Example 8 of the paper and its 
decomposition in the Fortran code and made a basic call to the
subroutine MYSUBROUTINE, which is bound to the C++ void function
'Sherman-Morrison();. For now compilation fails with lots of undefined
references.'
 2021-02-04 13:12:47 +01:00
François Coppens
090847247d Prepared the main Fortran infrastructure for the C++ calls. Updated the makefile. 2021-02-04 11:39:00 +01:00
François Coppens
5531d9eb12
Merge pull request #2 from fmgjcoppens/fix/upd-inverse 
Fix/upd inverse
 2021-02-03 15:05:01 +01:00
François Coppens
d03c9c665b Update of A0_inv fixed. matMul(...) breaks link between A0_inv and Slater_inv. Fixed by creating a new pointer that points to where Slater_inv points to before it gets reassigned by matMul(...) and then copy the updated elements back to the passed array pointed to by the new pointer. 2021-02-03 14:49:42 +01:00
François Coppens
aa6895a4aa Put helper functions in separate header file from the Sherman-Morrison algo. 2021-02-03 12:13:09 +01:00
François Coppens
1d9bb30abc
Merge pull request #1 from fmgjcoppens/fix/compile 
Problem fixed.
 2021-02-03 11:09:51 +01:00
François Coppens
68d27b6df6 Problem fixed: template function definitions (implementations) need to be fully known in the header file (.hpp) and not in the implementation file (.cpp). 2021-02-03 11:02:15 +01:00
François Coppens
7d55d7db77 Split the program in a header file and an implementation file and included them in main. Does not compile. Get the following error: ld: /tmp/icpcnmVxvw.o: in function void showMatrix<int>(int**, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' 2021-02-02 17:06:32 +01:00
François Coppens
9d47bf9bb3 Extracted the SM algorithm and wrote it as a void function that updates the passed old inverse. Does not work yet. For some reason the changes in the inverse do not persist when the function is finished. Also the inverse is not correct. 2021-02-02 15:08:41 +01:00
François Coppens
7d3ffe1d2a Added random matrix initialisation of arbitrary size. Added function to calculate determinant to test matrix invertability of A and A0. 2021-01-29 12:53:20 +01:00
François Coppens
8f54ca1124 Removed .vscode preferences dir from git index and added to .gitignore. 2021-01-29 10:23:22 +01:00
François Coppens
4c1b7f3098 Converted overloaded functions into templates. Removed second size argument from the showMatrix function since we are only interested in square matrices. 2021-01-29 10:03:07 +01:00
François Coppens
d45df44e5e C++ implementation of algo 3 is working. Not optimised yet. 2021-01-27 17:19:41 +01:00
François Coppens
e509f28ba6 That's it for today! 2021-01-26 16:27:57 +01:00