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Merge FAFOOM v2 #5

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f3c6417
starting to make modifications
Apr 4, 2017
4197ea8
vdW radii implementation
Apr 12, 2017
84613e7
I still not good at commits...(((
Apr 19, 2017
101cbcc
Added producing of 'valid' and 'invalid' folders for related structures.
Apr 19, 2017
d3502fc
Merge branch 'dmitrii-mod' of github.com:FHIBioGroup/fafoom-dev into …
Apr 19, 2017
76c485e
Including translation of the atom positions for str3d structure.
Apr 19, 2017
7159723
Implementation of Centroid degree of freedom. Centeroid of the molecu…
Apr 25, 2017
192cea4
Operations with lists substituted with operations with np.arrays.
Apr 26, 2017
57baf87
Centre of mass implemented
Apr 28, 2017
b05fb10
Tensor of inertia implemented for molecule from sdf_string (for str3d…
May 1, 2017
40e0d11
dirty quaternions are in.
May 30, 2017
21f3a93
Updated some ongoing chalenges with assinging of centroid and orienta…
Jun 2, 2017
a9ca446
Degrees of freedom are roughly implemented. Need to be tested and rev…
Jun 8, 2017
14398ea
adding test_and_examples folder
Jun 8, 2017
35b7333
Add files via upload
Jun 8, 2017
5427aa2
Jst fixing a typo
Jun 14, 2017
de23227
Typos really
Jun 14, 2017
9aff8ec
Add preprocessing script
Jun 22, 2017
a6ebd5a
Preprocessing folder
Jun 22, 2017
10a2733
Merge branch 'dmitrii-mod' of github.com:FHIBioGroup/fafoom-dev into …
Jun 22, 2017
d7c4b03
Preprocessing generator structures, improved centroid setting (for ex…
Jul 5, 2017
2def24a
try to add scripts for generating of valid structures.
Jul 5, 2017
a020e3f
try
Jul 5, 2017
e53d75f
Adjusting of the generated structures positions with respect to surro…
Jul 6, 2017
871e5b5
Try to commit from Atom. Pyforcefield added, generating inputs for MD
Jul 11, 2017
9638d72
ForceField works, generations are produced. Need to fix check for cla…
Jul 20, 2017
2dc361e
New test files
Jul 20, 2017
a08e82f
Start to replace RDkIT module.
Jul 27, 2017
ba071d1
update_coords_sdf, quaternion_measure now free of RDkit
Jul 27, 2017
adb8ab7
Ready to test dihedral test, seems to be okay
Jul 28, 2017
0c6e77a
Seems that measure.py is free of RDKit, but need to check closely pyr…
Jul 28, 2017
77f78ad
Utilities module is free from RDKit. Need to check Kabsh algorithm vs…
Jul 28, 2017
ba7be7a
Good Bye RDKit, now testing time!!! (pyff.py uses RDKit naturally, ne…
Jul 28, 2017
4990095
Daily update
Aug 17, 2017
084856e
Kabsh algorithm works fine without hydrogens, with hydrogens it is fo…
Aug 28, 2017
ec0b540
Seems that it is finally working
Sep 8, 2017
977373d
Also ga.py should be added
Sep 8, 2017
d917062
Add 'ga.py' outside
Sep 8, 2017
2390683
Try to clean a little bit first
Sep 12, 2017
8295a3e
Cleaning up
Sep 12, 2017
069319e
Cleaning up code a little bit. Need to check Reinitialization after r…
Sep 12, 2017
d48249c
prepare.py script is added in folder /scripts
Sep 13, 2017
41844e0
Preprocessing directory deleted for convinience
Sep 13, 2017
88cb989
Restructurization: bin folder should be added to path.
Sep 13, 2017
d732e2d
Exaple added, Scripts folder deleted. Improved obtaining of the lengt…
Sep 13, 2017
605e59b
Instructions for centroid optimization example added.
Sep 13, 2017
bdd9112
bin directory is not a good idea, now it should work.
Sep 13, 2017
f34c45f
Bug with obtaining of the length of the geometry.in.constrained file …
Sep 13, 2017
b112410
Prepare script now more user friendly.
Sep 14, 2017
1d49143
All RDkit dependencies are disabled in the main developed version (in…
Sep 15, 2017
b0514c1
Added flag crossover_method = single_point or random_points. Need to …
Sep 15, 2017
06a804b
Improved reinitialization after backup. Improved mutattions for centr…
Sep 18, 2017
2a3cd1c
Quick and dirty omplementation for adjusting too large distances
Sep 26, 2017
151fa09
Structures_gen.py Script is improved and ready to use.
Sep 28, 2017
4bfabab
Improved the behavior after not converged SCF cycle: folder is delet…
Sep 28, 2017
1570722
Start experimental GA with more than one molecule.
Sep 29, 2017
1048917
Minor changes related to execution and storage of results and to send…
Oct 11, 2017
1501cdc
Now Population is not decreasing after failed relaxations.
Oct 12, 2017
81653fe
Preparing for documentation and general update.
Oct 24, 2017
b62f400
Daily update
Oct 25, 2017
d61d009
Restart remastered. Backup file now can be used as starting point wit…
Oct 26, 2017
9b85419
Adjustment of the flag, that reduces criteria for vdW radii is added,…
Nov 1, 2017
9d84033
WhatsNew in Fafoom folder added for tracking
Nov 7, 2017
40ad59a
Lots of changes: Iterations counting are corrected, Output file made …
Nov 17, 2017
7e6b110
Protomeric Degree of freedom is now available: Generation of random s…
Nov 28, 2017
d3b4d2c
Protomeric state is ready. Need to chack 'right_order_to_assign' flag…
Nov 30, 2017
86012b1
Lot's of updates.
Feb 27, 2018
f63fe28
Correect naming of folders after restart
Feb 27, 2018
a040e6d
Fixing Adjustment of the molecule with respect to Ion in the origin
Mar 22, 2018
eb568a8
Untrack *.pyc files
Mar 22, 2018
88ff458
Delted unused fucnctions, stylistic errors improved, typos, just to m…
Mar 22, 2018
250a4d3
Typos corrected
Mar 28, 2018
b898f1f
Shared blacklist is implemented. Now only unique structures across di…
May 3, 2018
cd2e8f3
Small change test pycharm
Jun 23, 2018
3aec21c
Test commit after a while
Jun 23, 2018
d3e1238
Commented unfinished TESTOBject. Now should not raise an errorwqX
Jul 23, 2018
ed0abb1
Small changes to output
Jul 25, 2018
8932ec0
If there is no backup files produced - fafoom will clean directory pr…
Jul 25, 2018
72433ed
After restart fafoom the correct unfinished directory will be removed
Jul 25, 2018
489223a
Another restart options correction
Jul 25, 2018
b770ad8
Fixed bug of sorting of structures after restar
Jul 26, 2018
c0c271f
Automated production of final xyz file is added
Jul 27, 2018
0111e18
Fix of the last commit
Jul 27, 2018
e9a1375
Another fix
Jul 27, 2018
e23e0a2
Make it nice and finally work
Jul 27, 2018
293092e
Added script collect_strucutres.py, Minor changes in output
Jul 27, 2018
e5426a3
Change prepare.py scipt a little bit
Jul 29, 2018
4ae26b0
Blacklist update after GA part is corrected
Jul 29, 2018
7499bb2
Clean and store at correct moment for Aims
Jul 29, 2018
29b55b0
Small bug in restart fixed
Jul 29, 2018
600257d
Python environment for workshop is changed
Jul 29, 2018
bafdfd7
Typo
Jul 29, 2018
d0adcfb
Inconsistent spaces in prepare.py fixed
Jul 29, 2018
6dcba8f
IDENTANTION NIGHTMARE
Jul 29, 2018
e65f075
One more
Jul 29, 2018
03178fe
Molecule adjustment
Jul 29, 2018
644c740
Prepare.py changed
Aug 1, 2018
55d8b62
Routines for connectivity identifying
Aug 29, 2018
bad6b6b
Scripts folder with additional scripts for postprocessing is added.
Oct 17, 2018
ca14481
typo fixed.
Sep 2, 2019
be31b32
Cleaning up of the directory flag is added for faster testing.
Sep 2, 2019
ae71d3e
Multiple molecule generator first commit
Sep 10, 2019
67ac5cf
Multiple molecule generator intermediate commit before testing and cl…
Sep 30, 2019
b8aac08
typo
Sep 30, 2019
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6 changes: 6 additions & 0 deletions .idea/vcs.xml
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59 changes: 59 additions & 0 deletions Structures_gen_test/mol.sdf
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mol.xyz
OpenBabel08301800023D

27 26 0 0 1 0 0 0 0 0999 V2000
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-0.4177 -0.4523 2.0011 C 0 0 2 0 0 0 0 0 0 0 0 0
0.7719 0.5015 2.0045 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9271 0.1852 1.7722 O 0 0 0 0 0 0 0 0 0 0 0 0
0.4855 -1.6591 0.5873 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7722 -2.3728 1.3635 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1715 0.0114 1.3407 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0752 -0.5683 3.4020 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1791 -0.7951 4.6336 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5055 -2.1633 4.7846 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5168 -2.3800 3.7516 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8362 -2.3552 3.9069 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4220 -2.7206 5.0655 N 0 0 0 0 0 0 0 0 0 0 0 0
3.5943 -1.9640 2.8690 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.6345 0.3619 3.5671 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8342 -1.3649 3.3396 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8165 -0.6623 5.5204 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5875 -0.0065 4.6983 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2347 -2.9753 4.7291 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9711 -2.2192 5.7762 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1349 -2.2604 2.7746 H 0 0 0 0 0 0 0 0 0 0 0 0
4.4021 -2.5369 5.2333 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1825 -1.3218 2.1897 H 0 0 0 0 0 0 0 0 0 0 0 0
4.5886 -2.1467 2.8409 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9336 -3.3039 5.7317 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3915 1.7572 2.2885 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1864 2.3269 2.2623 H 0 0 0 0 0 0 0 0 0 0 0 0
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2 7 1 6 0 0 0
2 3 1 0 0 0 0
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3 26 1 0 0 0 0
4 3 2 0 0 0 0
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6 1 1 0 0 0 0
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16 8 1 0 0 0 0
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21 11 1 0 0 0 0
23 14 1 0 0 0 0
24 14 1 0 0 0 0
27 26 1 0 0 0 0
M END
$$$$
29 changes: 29 additions & 0 deletions Structures_gen_test/mol.xyz
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27

N 0.033102 -1.759436 1.497712
C -0.417682 -0.452299 2.001148
C 0.771911 0.501451 2.004516
O 1.927127 0.185203 1.772235
H 0.485536 -1.659132 0.587289
H -0.772213 -2.372805 1.363481
H -1.171481 0.011418 1.340683
C -1.075242 -0.568272 3.401975
C -0.179078 -0.795064 4.633565
C 0.505542 -2.163260 4.784602
N 1.516832 -2.380022 3.751597
C 2.836183 -2.355248 3.906886
N 3.421957 -2.720645 5.065496
N 3.594297 -1.964010 2.868998
H -1.634460 0.361921 3.567081
H -1.834242 -1.364862 3.339627
H -0.816514 -0.662256 5.520364
H 0.587508 -0.006511 4.698349
H -0.234715 -2.975294 4.729137
H 0.971096 -2.219184 5.776235
H 1.134879 -2.260392 2.774638
H 4.402090 -2.536892 5.233261
H 3.182548 -1.321808 2.189673
H 4.588565 -2.146737 2.840946
H 2.933605 -3.303893 5.731691
O 0.391491 1.757174 2.288528
H 1.186359 2.326859 2.262287
14 changes: 14 additions & 0 deletions WhatsNew/bibliography.bib
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@article{Blum2009,
abstract = {We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs. {\textcopyright} 2009 Elsevier B.V. All rights reserved.},
author = {Blum, Volker and Gehrke, Ralf and Hanke, Felix and Havu, Paula and Havu, Ville and Ren, Xinguo and Reuter, Karsten and Scheffler, Matthias},
doi = {10.1016/j.cpc.2009.06.022},
isbn = {0010-4655},
issn = {00104655},
journal = {Computer Physics Communications},
keywords = {Ab initio molecular simulations,Atom-centered basis functions,Density-functional theory,GW self-energy,Hartree-Fock,MP2,O(N) DFT},
number = {11},
pages = {2175--2196},
title = {{Ab initio molecular simulations with numeric atom-centered orbitals}},
volume = {180},
year = {2009}
}
30 changes: 30 additions & 0 deletions WhatsNew/main.aux
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\relax
\providecommand\hyper@newdestlabel[2]{}
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
\global\let\oldcontentsline\contentsline
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global\let\oldnewlabel\newlabel
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\ifx\hyper@anchor\@undefined
\let\contentsline\oldcontentsline
\let\newlabel\oldnewlabel
\fi}
\fi}
\global\let\hyper@last\relax
\gdef\HyperFirstAtBeginDocument#1{#1}
\providecommand\HyField@AuxAddToFields[1]{}
\providecommand\HyField@AuxAddToCoFields[2]{}
\@writefile{toc}{\contentsline {section}{\numberline {1}Fafoom 2.0.0}{2}{section.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}New external file: the surrounding which is not affected by GA}{2}{subsection.1.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}\textbf {New Degree of Freedom} \textit {Centroid}}{2}{subsection.1.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}\textbf {New Degree of Freedom:} \textit {Orientation}}{2}{subsection.1.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.4}\textbf {New keyword:} \textit {volume}}{3}{subsection.1.4}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.5}Geometry validation have been changed}{3}{subsection.1.5}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.6}Explicit specifying of \textit {list\_of\_torsion} is mandatory}{3}{subsection.1.6}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.7}Fafoom iterfaced with NAMD for geometry relaxations with "INTERFACE" Force Field}{3}{subsection.1.7}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.8}Blacklist representation is remastered}{4}{subsection.1.8}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.9}Minor changes}{4}{subsection.1.9}}
\@writefile{toc}{\contentsline {section}{\numberline {2}Original Fafoom 1.0.0}{5}{section.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Capabilities}{5}{subsection.2.1}}
101 changes: 101 additions & 0 deletions WhatsNew/main.fdb_latexmk
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