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Precommit: Format source_md #8190

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Precommit: Format source_md
Growl1234 Oct 30, 2026
d48da73
Alternative style
Growl1234 Oct 30, 2026
df40807
Reformat
Growl1234 Oct 30, 2026
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90 changes: 52 additions & 38 deletions .clang-format
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Original file line number Diff line number Diff line change
@@ -1,49 +1,63 @@
---
Language: Cpp
BasedOnStyle: Microsoft
BasedOnStyle: LLVM

AlwaysBreakTemplateDeclarations: Yes
ColumnLimit: 120

AllowAllArgumentsOnNextLine: false
AllowAllParametersOfDeclarationOnNextLine: false
#AlwaysBreakTemplateDeclarations: Yes
#
#AllowAllArgumentsOnNextLine: false
#AllowAllParametersOfDeclarationOnNextLine: false
BinPackArguments: false
BinPackParameters: false

BreakBeforeBinaryOperators: All
BreakBeforeTernaryOperators: true

Cpp11BracedListStyle: true
FixNamespaceComments: true

# InsertBraces: true # only for clang-format version15.0.0 or later

# About include
IncludeBlocks: Regroup
IncludeIsMainRegex: '([-_](test|unittest))?$'
IncludeIsMainSourceRegex: ''

PackArguments:
BinPack: UseBreakAfter
BreakAfter: 3
PackParameters:
BinPack: UseBreakAfter
BreakAfter: 3
#
#BreakBeforeBinaryOperators: None
#BreakBeforeTernaryOperators: true
BreakBeforeBraces: Allman
BreakAfterOpenBracketFunction: true
AlignAfterOpenBracket: DontAlign
#
#Cpp11BracedListStyle: true
#FixNamespaceComments: true
#
InsertBraces: true # only for clang-format version15.0.0 or later
#
## About include
#IncludeBlocks: Regroup
#IncludeIsMainRegex: '([-_](test|unittest))?$'
#IncludeIsMainSourceRegex: ''
#
IndentWidth: 4
IndentWrappedFunctionNames: true

# About Point
DerivePointerAlignment: false
PointerAlignment: Left

ReflowComments: true
SortIncludes: true
SortUsingDeclarations: true

# About space
SpaceAfterCStyleCast: false
SpaceAfterLogicalNot: false
SpaceBeforeRangeBasedForLoopColon: false
SpaceInEmptyParentheses: false
SpacesInAngles: false
SpacesInCStyleCastParentheses: false
SpacesInContainerLiterals: false
SpacesInParentheses: false
SpacesInSquareBrackets: false
#IndentWrappedFunctionNames: true
#
## About Point
#DerivePointerAlignment: false
#PointerAlignment: Left
PenaltyBreakBeforeMemberAccess: 1000
PenaltyBreakScopeResolution: 1000

#
#ReflowComments: true
#SortIncludes: true
#SortUsingDeclarations: true
#
## About space
#SpaceAfterCStyleCast: false
#SpaceAfterLogicalNot: false
#SpaceBeforeRangeBasedForLoopColon: false
#SpaceInEmptyParentheses: false
#SpacesInAngles: false
#SpacesInCStyleCastParentheses: false
#SpacesInContainerLiterals: false
#SpacesInParentheses: false
#SpacesInSquareBrackets: false
#
Standard: c++11
TabWidth: 4
UseTab: Never
Expand Down
139 changes: 98 additions & 41 deletions source/source_md/fire.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,19 @@
#endif
#include "source_base/timer.h"

FIRE::FIRE(const MD_para& mdp_in,
const bool cal_stress_in,
const bool init_vel,
const int my_rank_in,
const double force_thr_in,
MDCell& mdcell_in)
: MD_base(mdp_in, cal_stress_in, init_vel, my_rank_in, mdcell_in)
FIRE::FIRE(
const MD_para &mdp_in,
const bool cal_stress_in,
const bool init_vel,
const int my_rank_in,
const double force_thr_in,
MDCell &mdcell_in)
: MD_base(
mdp_in,
cal_stress_in,
init_vel,
my_rank_in,
mdcell_in)
{
force_thr = force_thr_in;
dt_max = -1.0;
Expand All @@ -32,11 +38,9 @@ FIRE::FIRE(const MD_para& mdp_in,
// force_thr = 1e-3;
}

FIRE::~FIRE()
{
}
FIRE::~FIRE() {}

void FIRE::setup(ModuleESolver::ESolver* p_esolver, const std::string& global_readin_dir, DomainDecomposition& decomp)
void FIRE::setup(ModuleESolver::ESolver *p_esolver, const std::string &global_readin_dir, DomainDecomposition &decomp)
{
ModuleBase::TITLE("FIRE", "setup");
ModuleBase::timer::start("FIRE", "setup");
Expand All @@ -50,7 +54,7 @@ void FIRE::setup(ModuleESolver::ESolver* p_esolver, const std::string& global_re
return;
}

void FIRE::first_half(std::ofstream& ofs)
void FIRE::first_half(std::ofstream &ofs)
{
ModuleBase::TITLE("FIRE", "first_half");
ModuleBase::timer::start("FIRE", "first_half");
Expand All @@ -66,7 +70,6 @@ void FIRE::first_half(std::ofstream& ofs)
return;
}


void FIRE::second_half(void)
{
ModuleBase::TITLE("FIRE", "second_half");
Expand All @@ -81,8 +84,7 @@ void FIRE::second_half(void)
return;
}


void FIRE::print_md(std::ofstream& ofs, const bool& cal_stress)
void FIRE::print_md(std::ofstream &ofs, const bool &cal_stress)
{
MD_base::print_md(ofs, cal_stress);

Expand All @@ -94,8 +96,7 @@ void FIRE::print_md(std::ofstream& ofs, const bool& cal_stress)
return;
}


void FIRE::write_restart(const std::string& global_out_dir)
void FIRE::write_restart(const std::string &global_out_dir)
{
if (!my_rank)
{
Expand All @@ -118,8 +119,7 @@ void FIRE::write_restart(const std::string& global_out_dir)
return;
}


void FIRE::restart(const std::string& global_readin_dir)
void FIRE::restart(const std::string &global_readin_dir)
{
bool ok = true;

Expand All @@ -137,16 +137,21 @@ void FIRE::restart(const std::string& global_readin_dir)
if (ok)
{
file >> step_rst_ >> md_tfirst >> alpha >> negative_count >> dt_max >> md_dt;
if(!file)
if (!file)
{
ok = false;
}
}
file.close();
}
}

#ifdef __MPI
MPI_Bcast(&ok, 1, MPI_C_BOOL, 0, mdcell.communicator());
MPI_Bcast(
&ok,
1,
MPI_C_BOOL,
0,
mdcell.communicator());
#endif

if (!ok)
Expand All @@ -155,12 +160,42 @@ void FIRE::restart(const std::string& global_readin_dir)
}

#ifdef __MPI
MPI_Bcast(&step_rst_, 1, MPI_INT, 0, mdcell.communicator());
MPI_Bcast(&md_tfirst, 1, MPI_DOUBLE, 0, mdcell.communicator());
MPI_Bcast(&alpha, 1, MPI_DOUBLE, 0, mdcell.communicator());
MPI_Bcast(&negative_count, 1, MPI_INT, 0, mdcell.communicator());
MPI_Bcast(&dt_max, 1, MPI_DOUBLE, 0, mdcell.communicator());
MPI_Bcast(&md_dt, 1, MPI_DOUBLE, 0, mdcell.communicator());
MPI_Bcast(
&step_rst_,
1,
MPI_INT,
0,
mdcell.communicator());
MPI_Bcast(
&md_tfirst,
1,
MPI_DOUBLE,
0,
mdcell.communicator());
MPI_Bcast(
&alpha,
1,
MPI_DOUBLE,
0,
mdcell.communicator());
MPI_Bcast(
&negative_count,
1,
MPI_INT,
0,
mdcell.communicator());
MPI_Bcast(
&dt_max,
1,
MPI_DOUBLE,
0,
mdcell.communicator());
MPI_Bcast(
&md_dt,
1,
MPI_DOUBLE,
0,
mdcell.communicator());
#endif

return;
Expand All @@ -172,7 +207,7 @@ void FIRE::check_force(void)

std::int64_t movable_dof = 0;

for (const LocalAtom& atom : mdcell.owned_atoms())
for (const LocalAtom &atom : mdcell.owned_atoms())
{
for (int j = 0; j < 3; ++j)
{
Expand All @@ -197,13 +232,25 @@ void FIRE::check_force(void)
}
}

#ifdef __MPI
#ifdef __MPI
if (mdcell.mpi_size() > 1)
{
double global_max = 0.0;
std::int64_t global_movable_dof = 0;
MPI_Allreduce(&max, &global_max, 1, MPI_DOUBLE, MPI_MAX, mdcell.communicator());
MPI_Allreduce(&movable_dof, &global_movable_dof, 1, MPI_INT64_T, MPI_SUM, mdcell.communicator());
MPI_Allreduce(
&max,
&global_max,
1,
MPI_DOUBLE,
MPI_MAX,
mdcell.communicator());
MPI_Allreduce(
&movable_dof,
&global_movable_dof,
1,
MPI_INT64_T,
MPI_SUM,
mdcell.communicator());
max = global_max;
movable_dof = global_movable_dof;
}
Expand All @@ -224,7 +271,6 @@ void FIRE::check_force(void)
return;
}


void FIRE::check_fire(void)
{
double P = 0.0;
Expand All @@ -242,7 +288,7 @@ void FIRE::check_fire(void)
// Compute P, |F| and |v| only on movable degrees of freedom.
// Fixed atoms/directions may have non-zero raw forces, but they should not
// affect the FIRE velocity projection or adaptive time-step control.
for (LocalAtom& atom : mdcell.owned_atoms())
for (LocalAtom &atom : mdcell.owned_atoms())
{
for (int j = 0; j < 3; ++j)
{
Expand All @@ -261,14 +307,26 @@ void FIRE::check_fire(void)
}
}

#ifdef __MPI
#ifdef __MPI
if (mdcell.mpi_size() > 1)
{
double local_values[3] = {P, sumforce, normvel};
double global_values[3] = {0.0, 0.0, 0.0};
std::int64_t global_movable_dof = 0;
MPI_Allreduce(local_values, global_values, 3, MPI_DOUBLE, MPI_SUM, mdcell.communicator());
MPI_Allreduce(&movable_dof, &global_movable_dof, 1, MPI_INT64_T, MPI_SUM, mdcell.communicator());
MPI_Allreduce(
local_values,
global_values,
3,
MPI_DOUBLE,
MPI_SUM,
mdcell.communicator());
MPI_Allreduce(
&movable_dof,
&global_movable_dof,
1,
MPI_INT64_T,
MPI_SUM,
mdcell.communicator());
P = global_values[0];
sumforce = global_values[1];
normvel = global_values[2];
Expand All @@ -289,7 +347,7 @@ void FIRE::check_fire(void)
// Avoid 0/0. In a truly converged case check_force() should stop the run.
if (sumforce > 0.0 && normvel > 0.0)
{
for (LocalAtom& atom : mdcell.owned_atoms())
for (LocalAtom &atom : mdcell.owned_atoms())
{
for (int j = 0; j < 3; ++j)
{
Expand All @@ -299,8 +357,7 @@ void FIRE::check_fire(void)
continue;
}

atom.vel[j] = (1.0 - alpha) * atom.vel[j]
+ alpha * atom.force[j] / sumforce * normvel;
atom.vel[j] = (1.0 - alpha) * atom.vel[j] + alpha * atom.force[j] / sumforce * normvel;
}
}
}
Expand All @@ -319,7 +376,7 @@ void FIRE::check_fire(void)
md_dt *= fdec;
negative_count = 0;

for (LocalAtom& atom : mdcell.owned_atoms())
for (LocalAtom &atom : mdcell.owned_atoms())
{
for (int j = 0; j < 3; ++j)
{
Expand Down
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