Skip to content

Refactor: replaced the original atomlink data structure with the Standard Template Library #5642

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 18 commits into from
Dec 2, 2024
Merged

Refactor: replaced the original atomlink data structure with the Standard Template Library #5642

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
06a49f4
A highly aggressive change: replaced the original atomlink data struc…
goodchong Nov 21, 2024
ad986d1
fix unittest errors
goodchong Nov 27, 2024
63a686c
[pre-commit.ci lite] apply automatic fixes
pre-commit-ci-lite[bot] Nov 28, 2024
4ec8064
fix a adj set clear bug and add self to adj list
goodchong Nov 28, 2024
d072dae
use vector to refactor Cellset varible
goodchong Nov 28, 2024
446c5cc
remove adjacent set, replaced by std list
goodchong Nov 28, 2024
489033f
remove set fatom
goodchong Nov 28, 2024
06bf2df
[pre-commit.ci lite] apply automatic fixes
pre-commit-ci-lite[bot] Nov 28, 2024
7c117b5
use 2 layers vector replace undered_map to improve perfermance
goodchong Nov 29, 2024
f36e661
remove a lot useless variable
goodchong Nov 29, 2024
98d86bb
Merge branch 'develop' into neighbor2
goodchong Nov 29, 2024
b5ffff8
remove some useless variables
goodchong Dec 2, 2024
2709779
refresh unit test to code logic
goodchong Dec 2, 2024
85f031a
Merge branch 'develop' into neighbor2
goodchong Dec 2, 2024
4afce26
[pre-commit.ci lite] apply automatic fixes
pre-commit-ci-lite[bot] Dec 2, 2024
c680655
Merge branch 'develop' into neighbor2
goodchong Dec 2, 2024
2d446fc
fix a bug to force quit when test
goodchong Dec 2, 2024
7f777c9
fresh unit test according to latest code logic
goodchong Dec 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions source/Makefile.Objects
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -366,8 +366,7 @@ OBJS_MD=fire.o\
run_md.o\
verlet.o\

OBJS_NEIGHBOR=sltk_adjacent_set.o\
sltk_atom.o\
OBJS_NEIGHBOR=sltk_atom.o\
sltk_atom_arrange.o\
sltk_atom_input.o\
sltk_grid.o\
Expand Down
1 change: 0 additions & 1 deletion source/module_cell/module_neighbor/CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
add_library(
neighbor
OBJECT
sltk_adjacent_set.cpp
sltk_atom.cpp
sltk_atom_arrange.cpp
sltk_atom_input.cpp
Expand Down
121 changes: 0 additions & 121 deletions source/module_cell/module_neighbor/sltk_adjacent_set.cpp
View file
Open in desktop

This file was deleted.

117 changes: 0 additions & 117 deletions source/module_cell/module_neighbor/sltk_adjacent_set.h
View file
Open in desktop

This file was deleted.

15 changes: 0 additions & 15 deletions source/module_cell/module_neighbor/sltk_atom.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,27 +1,12 @@
#include "sltk_atom.h"
#include <iostream>

class AdjacentSet;

//int FAtom::count1 = 0;
//int FAtom::count2 = 0;

/*** Constructors and destructor ***/
FAtom::FAtom()
{
d_x = 0.0;
d_y = 0.0;
d_z = 0.0;
as = nullptr;
type = 0;
natom = 0;
}

FAtom::~FAtom()
{
}

void FAtom::delete_vector(void)
{
if (as) { as->delete_vector(); }
}
42 changes: 14 additions & 28 deletions source/module_cell/module_neighbor/sltk_atom.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,8 @@

#include <memory>
#include "sltk_util.h"
#include "sltk_adjacent_set.h"

class AdjacentSet;
#include "module_base/timer.h"
#include <vector>

// a class contains the atom position,
// the type and the index,
Expand All @@ -15,7 +14,7 @@ class FAtom
double d_x;
double d_y;
double d_z;
std::shared_ptr<AdjacentSet> as;
std::vector<FAtom *> adjacent;

int type;
int natom;
Expand All @@ -42,30 +41,17 @@ class FAtom
cell_y = cell_y_in;
cell_z = cell_z_in;
}
~FAtom();
//2015-05-07
void delete_vector();

// static int count1;
// static int count2;

//==========================================================
// MEMBER FUNCTION :
// NAME : setAdjacent
// Dangerous but high performance interface function!
// no exception test.
//
// NAME : getAdjacentSet
//
// NAME : setAdjacentSet
//==========================================================

std::shared_ptr<AdjacentSet> getAdjacentSet() const
{ return this->as; }

void allocate_AdjacentSet()
{ this->as = std::make_shared<AdjacentSet>(); }
~FAtom()
{
adjacent.clear();
}

void addAdjacent(FAtom& atom_in)
{
adjacent.push_back( &atom_in);
}
const std::vector<FAtom *>& getAdjacent() const { return adjacent; }
void clearAdjacent() { adjacent.clear(); }
//==========================================================
// MEMBER FUNCTION :
// EXPLAIN : get value
Expand All @@ -77,7 +63,7 @@ class FAtom
const int& getNatom() const { return natom;}
const int& getCellX() const { return cell_x; }
const int& getCellY() const { return cell_y; }
const int& getCellZ() const { return cell_z; }
const int& getCellZ() const { return cell_z; }
};

#endif
Loading
Loading