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Piece wise remove topology item #486

Merged
merged 65 commits into from
Dec 24, 2019
Merged

Piece wise remove topology item #486

merged 65 commits into from
Dec 24, 2019

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JoshuaSBrown
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@JoshuaSBrown JoshuaSBrown commented Dec 21, 2019 •
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Remove unneeded topology item, removing backward pointer.
Added const correctness
Fixed header guards
added pragma once
removed unused beadtyp

@JoshuaSBrown
Remove topology item
cb5a69a
@JoshuaSBrown
removed bead type class
3c605ec
@JoshuaSBrown
Removed bead type include from topology class
f9a2a72
@JoshuaSBrown
Removed topology item include
663554e
@JoshuaSBrown
Corrected header guard in molecule.h
5e5b373
@JoshuaSBrown
Remove extra space
4f5b7ac
@JoshuaSBrown
Removed topology item parent
3d23b3e
@JoshuaSBrown
Corrected header in residue
940b43c
@JoshuaSBrown
Added pragma once to residue.h
0b14e30
@JoshuaSBrown
Corrected topology header guard
a19d898
@JoshuaSBrown
Added pragma once to topology.h
d55db68
@JoshuaSBrown
Added pragma once to molecule.h
819975d
@JoshuaSBrown
Remove topology item include and parent from residue
ac6d59e
@JoshuaSBrown
Removed topology item from molecule constructor
06d87f8
@JoshuaSBrown
Removed topology item from residue.h
48f1bec
@JoshuaSBrown
Corrected constructors for Molecule and Residue in topology.h
e0bb3e7
@JoshuaSBrown
Fix function calls in csg_gmxtopology
db5c53e
@JoshuaSBrown
Added const correctness
419fea8
@JoshuaSBrown
Added const correctness to methods in interaction.h
a00014d
@JoshuaSBrown
Corrected header guard
ae60c76
@JoshuaSBrown
Added pragma once to interaction.h
e30e0e0
@JoshuaSBrown
Added const correctness to Bonded Interactions method call
0d99821
@JoshuaSBrown
Added pragma once to within header guard
30fd548
@JoshuaSBrown
Removed getParent call from main.cc
367ba51
@JoshuaSBrown
Corrected typo in method name
aeaa6be
@JoshuaSBrown
Corrected typo
ae6b95d
@JoshuaSBrown
Fixed typo
7a0339d
@JoshuaSBrown
Pass boundary condtion to bead mapping apply function call, and creat…
70fc6b5 
…e method
@JoshuaSBrown
Merge branch 'master' into piece-wise-remove-topology-item
2a55c42
@JoshuaSBrown
Remove unneeded include from test
1ed1b69
@JoshuaSBrown
Merge branch 'piece-wise-remove-topology-item' of https://github.com/…
e0a8f3d 
…votca/csg into piece-wise-remove-topology-item
@JoshuaSBrown
Remove beadtype.h include
552dc3b
@JoshuaSBrown
Removed beadtype include from test_bead
83bd3c0
@JoshuaSBrown
Removed beadtype include from test_beadtriple
a86d3b9
@JoshuaSBrown
Removed beadtype from test_nblist_3body
0876040
@JoshuaSBrown
Removed beadtype from nblistgrid_3body
c156767
@JoshuaSBrown
Remove beadtype include from test_triplelist
2b2ab00
@JoshuaSBrown
Merge branch 'master' into piece-wise-remove-topology-item
9f6d4f1
@JoshuaSBrown
Made beadmap apply method safer for MapSphere
4c7adff
@JoshuaSBrown
Made Map_Ellipsoid Apply method safer, removed or statement
618309e
@JoshuaSBrown
Merge branch 'master' into piece-wise-remove-topology-item
656d9c3
@JoshuaSBrown
Remove topology item from basebead.h
32bfdec
@JoshuaSBrown
Fixed includes in test
182fcf2
@JoshuaSBrown
Update formatting boundarycondition.cc
9330b9a
@JoshuaSBrown
Fix formatting
5fe31d2
@junghans
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One of the many failed tests:

79/228 Test  #79: integration_Run_csg_fmatch .........................Child aborted***Exception:   0.16 sec
I have 648 beads in 216 molecules
I have 216 beads in 216 molecules for the coarsegraining
csg_fmatch: /builds/votca/csg/votca/csg/src/tools/../../include/votca/csg/basebead.h:158: virtual const Vector3d& votca::csg::BaseBead::getPos() const: Assertion `bead_position_set_ && "Cannot get bead position as it has not been set."' failed.

@JoshuaSBrown
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Ya, I don't know what's going on, I have yet to reproduce the errors...

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codecov bot commented Dec 23, 2019 •
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Codecov Report

Merging #486 into master will decrease coverage by 0.1%.
The diff coverage is 48.1%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master   #486     +/-   ##
=======================================
- Coverage    61.1%    61%   -0.2%     
=======================================
  Files         129    128      -1     
  Lines        6322   6342     +20     
=======================================
+ Hits         3869   3873      +4     
- Misses       2453   2469     +16
Flag Coverage Δ
#gcc 61% <48.1%> (-0.2%) ⬇️
Impacted Files Coverage Δ
include/votca/csg/map.h 80% <ø> (ø) ⬆️
include/votca/csg/boundarycondition.h 100% <ø> (ø) ⬆️
include/votca/csg/basebead.h 100% <ø> (ø) ⬆️
src/tools/csg_gmxtopol.cc 21.3% <0%> (ø) ⬆️
src/csg_boltzmann/main.cc 19.7% <0%> (+0.5%) ⬆️
src/libcsg/topology.cc 42.6% <0%> (-4.6%) ⬇️
include/votca/csg/molecule.h 84.6% <100%> (-1.1%) ⬇️
include/votca/csg/bead.h 69.6% <100%> (-0.9%) ⬇️
include/votca/csg/interaction.h 94% <100%> (ø) ⬆️
include/votca/csg/residue.h 100% <100%> (ø) ⬆️
... and 6 more

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@JoshuaSBrown
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ping @JensWehner

@junghans junghans merged commit 0c458e9 into master Dec 24, 2019
@junghans junghans deleted the piece-wise-remove-topology-item branch December 24, 2019 18:12
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@JensWehner JensWehner JensWehner approved these changes

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@JoshuaSBrown @junghans @JensWehner