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Fix JSON coordinate units #7760

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Merged
mohanchen merged 2 commits into from
Aug 2, 2026
Merged

Fix JSON coordinate units #7760

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2b5795f
Fix JSON coordinate units
MoseyQAQ Aug 2, 2026
b746b87
Fix JSON cell units
MoseyQAQ Aug 2, 2026
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2 changes: 1 addition & 1 deletion docs/advanced/json/json_para.md
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ An array of dicts, including information about each self-consistent field (SCF)
- `force` - [array(array(double))] The forces calculated on each atom. Unit in eV/Angstrom.
- `stress` - [array(array(double))] The stress tensor. Unit in Kbar.
- `cell` - [array(array(double))] The cell parameters. Unit in Angstrom.
- `coordinate` - [array(array(double))] The coordinates of the atoms in the box after the simulation.
- `coordinate` - [array(array(double))] The coordinates of the atoms in the box after the simulation. Unit in Angstrom.
- `total_mag` , `absolute_mag` , `mag` - [double] The total magnetic moment; total absolute magnetic moment; and a list of magnetic moments for each atom, respectively.
- `scf_converge` - [bool] A boolean indicating whether the scf optimization has converged.
- `scf` - [array(object(str:double)] A list of each scf step, each item contains:
Expand Down
26 changes: 13 additions & 13 deletions source/source_io/module_json/init_info.cpp
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Expand Up @@ -98,7 +98,7 @@ void gen_stru(UnitCell* ucell)
}

// atom coordinate, mag and label
double lat0 = ucell->lat0;
const double lat0_angstrom = ucell->lat0_angstrom;
std::string* label = ucell->atom_label.data();
for (int i = 0; i < ntype; i++)
{
Expand All @@ -107,9 +107,9 @@ void gen_stru(UnitCell* ucell)
for (int j = 0; j < na; j++)
{
Json::jsonValue coordinateArray(JarrayType);
coordinateArray.JPushBack(tau[j][0] * lat0);
coordinateArray.JPushBack(tau[j][1] * lat0);
coordinateArray.JPushBack(tau[j][2] * lat0);
coordinateArray.JPushBack(tau[j][0] * lat0_angstrom);
coordinateArray.JPushBack(tau[j][1] * lat0_angstrom);
coordinateArray.JPushBack(tau[j][2] * lat0_angstrom);
Json::AbacusJson::add_json({"init", "coordinate"}, coordinateArray, true);
// Json::AbacusJson::add_Json(coordinateArray,true,"init","coordinate");

Expand All @@ -128,15 +128,15 @@ void gen_stru(UnitCell* ucell)
Json::jsonValue cellArray1(JarrayType);
Json::jsonValue cellArray2(JarrayType);
Json::jsonValue cellArray3(JarrayType);
cellArray1.JPushBack(ucell->latvec.e11);
cellArray1.JPushBack(ucell->latvec.e12);
cellArray1.JPushBack(ucell->latvec.e13);
cellArray2.JPushBack(ucell->latvec.e21);
cellArray2.JPushBack(ucell->latvec.e22);
cellArray2.JPushBack(ucell->latvec.e23);
cellArray3.JPushBack(ucell->latvec.e31);
cellArray3.JPushBack(ucell->latvec.e32);
cellArray3.JPushBack(ucell->latvec.e33);
cellArray1.JPushBack(ucell->latvec.e11 * lat0_angstrom);
cellArray1.JPushBack(ucell->latvec.e12 * lat0_angstrom);
cellArray1.JPushBack(ucell->latvec.e13 * lat0_angstrom);
cellArray2.JPushBack(ucell->latvec.e21 * lat0_angstrom);
cellArray2.JPushBack(ucell->latvec.e22 * lat0_angstrom);
cellArray2.JPushBack(ucell->latvec.e23 * lat0_angstrom);
cellArray3.JPushBack(ucell->latvec.e31 * lat0_angstrom);
cellArray3.JPushBack(ucell->latvec.e32 * lat0_angstrom);
cellArray3.JPushBack(ucell->latvec.e33 * lat0_angstrom);
Json::AbacusJson::add_json({"init", "cell"}, cellArray1, true);
Json::AbacusJson::add_json({"init", "cell"}, cellArray2, true);
Json::AbacusJson::add_json({"init", "cell"}, cellArray3, true);
Expand Down
26 changes: 13 additions & 13 deletions source/source_io/module_json/output_info.cpp
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Expand Up @@ -92,15 +92,15 @@ namespace Json
}
//add coordinate
int ntype = ucell->ntype;
double lat0 = ucell->lat0;
const double lat0_angstrom = ucell->lat0_angstrom;
for(int i=0;i<ntype;i++){
ModuleBase::Vector3<double>* tau = ucell->atoms[i].tau.data();
int na = ucell->atoms[i].na;
for(int j=0;j<na;j++){
Json::jsonValue coordinateArray(JarrayType);
coordinateArray.JPushBack(tau[j][0]*lat0);
coordinateArray.JPushBack(tau[j][1]*lat0);
coordinateArray.JPushBack(tau[j][2]*lat0);
coordinateArray.JPushBack(tau[j][0] * lat0_angstrom);
coordinateArray.JPushBack(tau[j][1] * lat0_angstrom);
coordinateArray.JPushBack(tau[j][2] * lat0_angstrom);
Json::AbacusJson::add_json({"output",-1,"coordinate"}, coordinateArray,true);
Json::AbacusJson::add_json( {"output",-1,"mag"},ucell->atoms[i].mag[j],true);
}
Expand All @@ -111,15 +111,15 @@ namespace Json
Json::jsonValue cellArray1(JarrayType);
Json::jsonValue cellArray2(JarrayType);
Json::jsonValue cellArray3(JarrayType);
cellArray1.JPushBack(ucell->latvec.e11);
cellArray1.JPushBack(ucell->latvec.e12);
cellArray1.JPushBack(ucell->latvec.e13);
cellArray2.JPushBack(ucell->latvec.e21);
cellArray2.JPushBack(ucell->latvec.e22);
cellArray2.JPushBack(ucell->latvec.e23);
cellArray3.JPushBack(ucell->latvec.e31);
cellArray3.JPushBack(ucell->latvec.e32);
cellArray3.JPushBack(ucell->latvec.e33);
cellArray1.JPushBack(ucell->latvec.e11 * lat0_angstrom);
cellArray1.JPushBack(ucell->latvec.e12 * lat0_angstrom);
cellArray1.JPushBack(ucell->latvec.e13 * lat0_angstrom);
cellArray2.JPushBack(ucell->latvec.e21 * lat0_angstrom);
cellArray2.JPushBack(ucell->latvec.e22 * lat0_angstrom);
cellArray2.JPushBack(ucell->latvec.e23 * lat0_angstrom);
cellArray3.JPushBack(ucell->latvec.e31 * lat0_angstrom);
cellArray3.JPushBack(ucell->latvec.e32 * lat0_angstrom);
cellArray3.JPushBack(ucell->latvec.e33 * lat0_angstrom);
Json::AbacusJson::add_json({"output",-1,"cell"}, cellArray1,true);
Json::AbacusJson::add_json({"output",-1,"cell"}, cellArray2,true);
Json::AbacusJson::add_json({"output",-1,"cell"}, cellArray3,true);
Expand Down
36 changes: 21 additions & 15 deletions source/source_io/module_json/test/para_json_test.cpp
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Expand Up @@ -7,6 +7,7 @@
#include "source_io/module_json/readin_info.h"
#include "source_io/module_parameter/parameter.h"
#include "source_io/module_json/para_json.h"
#include "source_base/constants.h"
#include "source_base/version.h"
#undef private
/************************************************
Expand Down Expand Up @@ -326,6 +327,7 @@ TEST(AbacusJsonTest, Init_stru_test)
ucell.atoms = atomlist;
ucell.atom_label.resize(1);
ucell.lat0 = lat0;
ucell.lat0_angstrom = lat0 * ModuleBase::BOHR_TO_A;

ModuleBase::Vector3<double> tau[2];

Expand Down Expand Up @@ -364,19 +366,23 @@ TEST(AbacusJsonTest, Init_stru_test)
ASSERT_EQ(Json::AbacusJson::doc["init"]["coordinate"][0][1].GetDouble(), 0);
ASSERT_EQ(Json::AbacusJson::doc["init"]["coordinate"][0][2].GetDouble(), 0);

ASSERT_EQ(Json::AbacusJson::doc["init"]["coordinate"][1][0].GetDouble(), 1.0);
ASSERT_EQ(Json::AbacusJson::doc["init"]["coordinate"][1][1].GetDouble(), 1.0);
ASSERT_EQ(Json::AbacusJson::doc["init"]["coordinate"][1][2].GetDouble(), 1.0);

ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][0][0].GetDouble(), 0.1);
ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][0][1].GetDouble(), 0.1);
ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][0][2].GetDouble(), 0.1);

ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][1][0].GetDouble(), 0.2);
ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][1][1].GetDouble(), 0.2);
ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][1][2].GetDouble(), 0.2);

ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][2][0].GetDouble(), 0.3);
ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][2][1].GetDouble(), 0.3);
ASSERT_EQ(Json::AbacusJson::doc["init"]["cell"][2][2].GetDouble(), 0.3);
EXPECT_NEAR(Json::AbacusJson::doc["init"]["coordinate"][1][0].GetDouble(),
ModuleBase::BOHR_TO_A,
1.0e-12);
EXPECT_NEAR(Json::AbacusJson::doc["init"]["coordinate"][1][1].GetDouble(),
ModuleBase::BOHR_TO_A,
1.0e-12);
EXPECT_NEAR(Json::AbacusJson::doc["init"]["coordinate"][1][2].GetDouble(),
ModuleBase::BOHR_TO_A,
1.0e-12);

for (int i = 0; i < 3; ++i)
{
for (int j = 0; j < 3; ++j)
{
EXPECT_NEAR(Json::AbacusJson::doc["init"]["cell"][i][j].GetDouble(),
(i + 1) * ModuleBase::BOHR_TO_A,
1.0e-12);
}
}
}
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