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merged 5 commits into from
Jul 10, 2025
Merged

Improve md calculation stress output in running log #6366

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5f0c35b
Improve md calculation stress output in running log
lanshuyue Jul 8, 2025
324fd59
Module_IO Unittest modify
lanshuyue Jul 8, 2025
155a128
ModuleMD Unittests modify
lanshuyue Jul 9, 2025
af0d195
modify code comment in fire_test.cpp
lanshuyue Jul 9, 2025
10f8f80
maintain setprecision(8) for md stress output
lanshuyue Jul 9, 2025
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6 changes: 3 additions & 3 deletions source/source_io/output_log.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -285,8 +285,8 @@ void print_stress(const std::string& name, const ModuleBase::matrix& scs,
}
else
{
title += " (KBAR)";
unit = " KBAR";
title += " (kbar)";
unit = " kbar";
unit_transform = ModuleBase::RYDBERG_SI / pow(ModuleBase::BOHR_RADIUS_SI, 3) * 1.0e-8;
}
std::vector<double> stress_x;
Expand Down Expand Up @@ -317,7 +317,7 @@ void print_stress(const std::string& name, const ModuleBase::matrix& scs,
fmt << stress_x << stress_y << stress_z;
table = fmt.str();
ofs << table;
if (name == "TOTAL-STRESS")
if (name == "TOTAL-STRESS" && PARAM.inp.calculation != "md")
{
ofs << " #TOTAL-PRESSURE# (EXCLUDE KINETIC PART OF IONS): " << std::fixed
<< std::setprecision(6) << pressure << unit
Expand Down
4 changes: 2 additions & 2 deletions source/source_io/test/outputlog_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -292,7 +292,7 @@ TEST(PrintStress, PrintStress)
std::string output_str;
getline(ifs, output_str);
getline(ifs, output_str); // mohan add 2025-06-22
EXPECT_THAT(output_str, testing::HasSubstr(" #TOTAL-STRESS (KBAR)#"));
EXPECT_THAT(output_str, testing::HasSubstr(" #TOTAL-STRESS (kbar)#"));

getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr("----------------------------------------------------------------"));
Expand All @@ -316,7 +316,7 @@ TEST(PrintStress, PrintStress)
EXPECT_THAT(output_str, testing::HasSubstr("----------------------------------------------------------------"));

getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" #TOTAL-PRESSURE# (EXCLUDE KINETIC PART OF IONS): 49035.075992 KBAR"));
EXPECT_THAT(output_str, testing::HasSubstr(" #TOTAL-PRESSURE# (EXCLUDE KINETIC PART OF IONS): 49035.075992 kbar"));
ifs.close();
std::remove("running_stress.txt");
}
Expand Down
14 changes: 8 additions & 6 deletions source/source_md/md_base.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -186,6 +186,13 @@ void MD_base::print_md(std::ofstream& ofs, const bool& cal_stress)
// running_log output
ofs.unsetf(std::ios::fixed);
ofs << std::setprecision(8);

if (cal_stress)
{
MD_func::print_stress(ofs, virial, stress);
ofs << std::endl;
}

ofs << " ------------------------------------------------------------------------------------------------"
<< std::endl;
ofs << " " << std::left << std::setw(20) << "Energy (Ry)" << std::left << std::setw(20) << "Potential (Ry)"
Expand All @@ -209,12 +216,7 @@ void MD_base::print_md(std::ofstream& ofs, const bool& cal_stress)
ofs << std::endl;
ofs << " ------------------------------------------------------------------------------------------------"
<< std::endl;

if (cal_stress)
{
MD_func::print_stress(ofs, virial, stress);
}

ofs << std::endl;
return;
}

Expand Down
3 changes: 2 additions & 1 deletion source/source_md/md_func.cpp
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Expand Up @@ -300,9 +300,10 @@ void print_stress(std::ofstream& ofs, const ModuleBase::matrix& virial, const Mo

const double unit_transform = ModuleBase::HARTREE_SI / pow(ModuleBase::BOHR_RADIUS_SI, 3) * 1.0e-8;

ofs << " MD PRESSURE (ELECTRONS+IONS) : " << stress_scalar * unit_transform << " kbar" << std::endl;

ofs << " ELECTRONIC PART OF STRESS: " << virial_scalar * unit_transform << " kbar" << std::endl;
ofs << " IONIC (KINETIC) PART OF STRESS: " << (stress_scalar - virial_scalar) * unit_transform << " kbar" << std::endl;
ofs << " MD PRESSURE (ELECTRONS+IONS) : " << stress_scalar * unit_transform << " kbar" << std::endl;

// one should use 'print_stress' function in ../source/source_io/output_log.cpp
/*
Expand Down
27 changes: 7 additions & 20 deletions source/source_md/test/fire_test.cpp
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Expand Up @@ -184,44 +184,31 @@ TEST_F(FIREtest, PrintMD)
std::ifstream ifs("running_fire.log");
std::string output_str;

// Line 1
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" ELECTRONIC PART OF STRESS: 0.24609992 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" IONIC (KINETIC) PART OF STRESS: 0.83853919 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" MD PRESSURE (ELECTRONS+IONS) : 1.0846391 kbar"));
getline(ifs, output_str);
getline(ifs, output_str);
EXPECT_THAT(output_str,
testing::HasSubstr(
" ------------------------------------------------------------------------------------------------"));

// Line 2
getline(ifs, output_str);
EXPECT_THAT(output_str,
testing::HasSubstr(
" Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) "));

// Line 3
getline(ifs, output_str);
EXPECT_THAT(output_str,
testing::HasSubstr(
" -0.015365236 -0.023915637 0.0085504016 300 1.0846391 "));

// Line 4
getline(ifs, output_str);
EXPECT_THAT(
output_str,
testing::HasSubstr(
" ------------------------------------------------------------------------------------------------"));

// Line 5
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" MD PRESSURE (ELECTRONS+IONS) : 1.0846391 kbar"));

// Line 6
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" ELECTRONIC PART OF STRESS: 0.24609992 kbar"));

// Line 7
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" IONIC (KINETIC) PART OF STRESS: 0.83853919 kbar"));

// Line 8
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" LARGEST FORCE (eV/A) : 0.049479926"));

Expand Down
7 changes: 7 additions & 0 deletions source/source_md/test/langevin_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,13 @@ TEST_F(Langevin_test, print_md)

std::ifstream ifs("running_langevin.log");
std::string output_str;
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" ELECTRONIC PART OF STRESS: 0.24609992 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" IONIC (KINETIC) PART OF STRESS: 0.83853919 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" MD PRESSURE (ELECTRONS+IONS) : 1.0846391 kbar"));
getline(ifs, output_str);
getline(ifs, output_str);
EXPECT_THAT(
output_str,
Expand Down
4 changes: 2 additions & 2 deletions source/source_md/test/md_func_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -385,11 +385,11 @@ TEST_F(MD_func_test, print_stress)
std::ifstream ifs("running.log");
std::string output_str;
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr("MD PRESSURE (ELECTRONS+IONS) : 0 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr("ELECTRONIC PART OF STRESS: 0 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr("IONIC (KINETIC) PART OF STRESS: 0 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr("MD PRESSURE (ELECTRONS+IONS) : 0 kbar"));
/*
getline(ifs, output_str);
getline(ifs, output_str);
Expand Down
7 changes: 7 additions & 0 deletions source/source_md/test/msst_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -225,6 +225,13 @@ TEST_F(MSST_test, print_md)

std::ifstream ifs("running_msst.log");
std::string output_str;
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" ELECTRONIC PART OF STRESS: 0.24609992 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" IONIC (KINETIC) PART OF STRESS: 0.8301538 kbar")); // result different from other MD methods
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" MD PRESSURE (ELECTRONS+IONS) : 1.0762537 kbar")); // result different from other MD methods
getline(ifs, output_str);
getline(ifs, output_str);
EXPECT_THAT(
output_str,
Expand Down
7 changes: 7 additions & 0 deletions source/source_md/test/nhchain_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -215,6 +215,13 @@ TEST_F(NHC_test, print_md)

std::ifstream ifs("running_nhchain.log");
std::string output_str;
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" ELECTRONIC PART OF STRESS: 0.24609992 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" IONIC (KINETIC) PART OF STRESS: 0.83853919 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" MD PRESSURE (ELECTRONS+IONS) : 1.0846391 kbar"));
getline(ifs, output_str);
getline(ifs, output_str);
EXPECT_THAT(
output_str,
Expand Down
7 changes: 7 additions & 0 deletions source/source_md/test/verlet_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -310,6 +310,13 @@ TEST_F(Verlet_test, print_md)

std::ifstream ifs("running_verlet.log");
std::string output_str;
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" ELECTRONIC PART OF STRESS: 0.24609992 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" IONIC (KINETIC) PART OF STRESS: 0.83853919 kbar"));
getline(ifs, output_str);
EXPECT_THAT(output_str, testing::HasSubstr(" MD PRESSURE (ELECTRONS+IONS) : 1.0846391 kbar"));
getline(ifs, output_str);
getline(ifs, output_str);
EXPECT_THAT(
output_str,
Expand Down
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