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feat(md): add thermodynamic output frequency #8160

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1021a75
feat(md): add thermodynamic output frequency
Oct 16, 2026
19f64d4
refactor(md): remove per-atom force output from md log
Oct 18, 2026
32e94cd
test(md): collect MD forces from trajectory dump
Oct 18, 2026
4a0bdfe
test(ofdft): dump forces for short MD cases
Oct 18, 2026
91ac9d8
fix(md): gate restart thermodynamic output
Oct 20, 2026
e23e031
Merge remote-tracking branch 'origin/develop' into feature/md-thermo-…
Oct 20, 2026
f45fa74
Merge origin/develop into feature/md-thermo-output
Oct 20, 2026
b9a2c63
Merge remote-tracking branch 'origin/develop' into feature/md-thermo-…
Oct 21, 2026
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60 changes: 0 additions & 60 deletions source/source_io/module_output/output_log.cpp
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Expand Up @@ -7,8 +7,6 @@
#include "source_base/global_variable.h"
#include "source_base/parallel_reduce.h"
#include "source_base/parallel_comm.h"
#include "source_cell/mdcell.h"

#include <cmath>
#include <iomanip>

Expand Down Expand Up @@ -286,64 +284,6 @@ void print_force(std::ofstream& ofs_running,
}
}

void print_force(std::ofstream& ofs, const MDCell& cell, const std::string& name)
{
const double output_acc = 1.0e-8;
const double force_unit = ModuleBase::Hartree_to_eV / ModuleBase::BOHR_TO_A;
const std::vector<LocalAtom>& owned_atoms = cell.owned_atoms();
const std::vector<std::string>& type_labels = cell.type_labels();

const auto print_atom = [&ofs, &type_labels, output_acc, force_unit](const LocalAtom& atom) {
const std::string& label = type_labels[static_cast<std::size_t>(atom.type)];
const double fx = std::abs(atom.force.x) > output_acc ? atom.force.x * force_unit : 0.0;
const double fy = std::abs(atom.force.y) > output_acc ? atom.force.y * force_unit : 0.0;
const double fz = std::abs(atom.force.z) > output_acc ? atom.force.z * force_unit : 0.0;
ofs << std::setw(9) << label + std::to_string(atom.type_index + 1)
<< std::setw(20) << std::fixed << std::setprecision(10) << fx
<< std::setw(20) << fy << std::setw(20) << fz << std::endl;
};

#ifdef __MPI
int rank = 0;
int size = 1;
MPI_Comm_rank(cell.communicator(), &rank);
MPI_Comm_size(cell.communicator(), &size);
if (rank != 0)
{
const int nowned_atoms = cell.owned_atoms().size();
MPI_Send(&nowned_atoms, 1, MPI_INT, 0, 0, cell.communicator());
for (const LocalAtom& atom : owned_atoms)
{
MPI_Send(&atom.type, 1, MPI_INT, 0, 1, cell.communicator());
MPI_Send(&atom.type_index, 1, MPI_INT64_T, 0, 2, cell.communicator());
MPI_Send(&atom.force.x, 3, MPI_DOUBLE, 0, 3, cell.communicator());
}
return;
}
#endif

ofs << "\n #" << name << "#" << std::endl;
ofs << std::setw(9) << "Atoms" << std::setw(20) << "Force_x" << std::setw(20)
<< "Force_y" << std::setw(20) << "Force_z" << std::endl;
for (const LocalAtom& atom : owned_atoms) print_atom(atom);

#ifdef __MPI
for (int source = 1; source < size; ++source)
{
int nlocal = 0;
MPI_Recv(&nlocal, 1, MPI_INT, source, 0, cell.communicator(), MPI_STATUS_IGNORE);
for (int iat = 0; iat < nlocal; ++iat)
{
LocalAtom atom;
MPI_Recv(&atom.type, 1, MPI_INT, source, 1, cell.communicator(), MPI_STATUS_IGNORE);
MPI_Recv(&atom.type_index, 1, MPI_INT64_T, source, 2, cell.communicator(), MPI_STATUS_IGNORE);
MPI_Recv(&atom.force.x, 3, MPI_DOUBLE, source, 3, cell.communicator(), MPI_STATUS_IGNORE);
print_atom(atom);
}
}
#endif
}

void print_stress(const std::string& name, const ModuleBase::matrix& scs,
const bool screen, const bool ry, std::ofstream &ofs)
{
Expand Down
8 changes: 0 additions & 8 deletions source/source_io/module_output/output_log.h
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Expand Up @@ -7,8 +7,6 @@
#include "source_base/matrix.h"
#include "source_cell/unitcell.h"

class MDCell;

namespace elecstate
{
struct Efermi;
Expand Down Expand Up @@ -67,12 +65,6 @@ void print_force(std::ofstream& ofs,
const ModuleBase::matrix& force,
bool ry = true);

/// @brief output forces stored on locally owned atoms of an MDCell
/// @param ofs the output stream on rank zero
/// @param cell the MD cell
/// @param name force term name
void print_force(std::ofstream& ofs, const MDCell& cell, const std::string& name);

/// @brief output stress components
/// @param name stress term name
/// @param f stress components
Expand Down
2 changes: 1 addition & 1 deletion source/source_io/module_parameter/md_parameter.h
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Expand Up @@ -19,9 +19,9 @@ struct MD_para
double md_tfirst = -1.0; ///< Temperature (in Hartree, 1 Hartree ~ 3E5 K)
double md_tlast = -1.0; ///< Target temperature
int md_dumpfreq = 1; ///< The period to dump MD information
int md_thermo_freq = 1; ///< The period to output MD thermodynamic information
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double md_neighbor_skin = 0.0; ///< Extra neighbor-list radius in Angstrom for MDCell solvers
int md_restartfreq = 5; ///< The period to output MD restart information
bool md_out_force = true; ///< output all atomic forces into running_md.log
int md_seed = -1; ///< random seed for MD
int md_prec_level = 0; ///< precision level for vc-md

Expand Down
23 changes: 11 additions & 12 deletions source/source_io/module_parameter/read_input_item_md.cpp
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Expand Up @@ -186,6 +186,17 @@ Note that md_tlast is only used in NVT/NPT simulations. If md_tlast is unset or
read_sync_int(input.mdp.md_dumpfreq);
this->add_item(item);
}
{
Input_Item item("md_thermo_freq");
item.annotation = "The period to output MD thermodynamic information";
item.category = "Molecular dynamics";
item.type = "Integer";
item.description = "The output frequency of MD step, energy, temperature, and pressure information in OUT.${suffix}/running_md.log and on screen. Set to 0 to disable this output.";
item.default_value = "1";
item.unit = "";
read_sync_int(input.mdp.md_thermo_freq);
this->add_item(item);
}
{
Input_Item item("md_neighbor_skin");
item.annotation = "extra MDCell neighbor-list radius";
Expand All @@ -200,18 +211,6 @@ Note that md_tlast is only used in NVT/NPT simulations. If md_tlast is unset or
read_sync_double(input.mdp.md_neighbor_skin);
this->add_item(item);
}
{
Input_Item item("md_out_force");

@Critsium-xy Critsium-xy Oct 26, 2026 •
edited
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Removing md_out_force (shipped in v3.11.0-beta9..11) makes inputs containing it abort, and the MDCell path no longer writes forces to running_md.log. Please state this and the dump_force/md_dumpfreq replacement in the PR description, together with the new md_thermo_freq.

item.annotation = "output all atomic forces into running_md.log or not";
item.category = "Molecular dynamics";
item.type = "Boolean";
item.description = "Whether to output the TOTAL-FORCE table in OUT.${suffix}/running_md.log for MDCell molecular dynamics. This does not affect force calculation or molecular dynamics integration.";
item.default_value = "True";
item.unit = "";
item.set_availability("");
read_sync_bool(input.mdp.md_out_force);
this->add_item(item);
}
{
Input_Item item("dump_force");
item.annotation = "output atomic forces into the file MD_dump or not";
Expand Down
2 changes: 1 addition & 1 deletion source/source_io/test/read_input_ptest.cpp
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Expand Up @@ -403,6 +403,7 @@ TEST_F(InputParaTest, ParaRead)
EXPECT_EQ(param.inp.mdp.md_damp, 1);
EXPECT_EQ(param.inp.mdp.md_dt, 1);
EXPECT_EQ(param.inp.mdp.md_dumpfreq, 1);
EXPECT_EQ(param.inp.mdp.md_thermo_freq, 1);
EXPECT_EQ(param.inp.mdp.md_nraise, 1);
EXPECT_EQ(param.inp.cal_syns[0], 0);
EXPECT_EQ(param.inp.cal_syns[1], 8);
Expand All @@ -416,7 +417,6 @@ TEST_F(InputParaTest, ParaRead)
EXPECT_EQ(param.inp.mdp.md_pmode, "iso");
EXPECT_EQ(param.inp.mdp.md_restart, 0);
EXPECT_EQ(param.inp.mdp.md_restartfreq, 5);
EXPECT_FALSE(param.inp.mdp.md_out_force);
EXPECT_FALSE(param.inp.mdp.plumed);
EXPECT_EQ(param.inp.mdp.plumed_file, "plumed.dat");
EXPECT_EQ(param.inp.mdp.md_seed, -1);
Expand Down
2 changes: 1 addition & 1 deletion source/source_io/test/support/INPUT
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Expand Up @@ -186,8 +186,8 @@ md_tchain 1 #number of Nose-Hoover chains
md_tfirst -1 #temperature first
md_tlast -1 #temperature last
md_dumpfreq 1 #The period to dump MD information
md_thermo_freq 1 #The period to output MD thermodynamic information
md_restartfreq 5 #The period to output MD restart information
md_out_force 0 #output all atomic forces into running_md.log or not
md_seed -1 #random seed for MD
md_prec_level 2 #precision level for vc-md
ref_cell_factor 1.0 #construct a reference cell bigger than the initial cell (currently disabled, must be 1.0)
Expand Down
6 changes: 6 additions & 0 deletions source/source_io/test_serial/read_input_item_test.cpp
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Expand Up @@ -2364,6 +2364,12 @@ TEST_F(InputTest, Item_test2)
it->second.reset_value(it->second, param);
EXPECT_EQ(TestParameters::input(param).mdp.md_nstep, 50);
}
{ // md_thermo_freq
auto it = find_label("md_thermo_freq", readinput.input_lists);
it->second.str_values = {"100"};
it->second.read_value(it->second, param);
EXPECT_EQ(TestParameters::input(param).mdp.md_thermo_freq, 100);
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}
{ // md_prec_level
auto it = find_label("md_prec_level", readinput.input_lists);
TestParameters::input(param).mdp.md_prec_level = 1;
Expand Down
10 changes: 1 addition & 9 deletions source/source_md/md_base.cpp
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Expand Up @@ -4,7 +4,6 @@
#ifdef __MPI
#include "mpi.h"
#endif
#include "source_io/module_output/print_info.h"
#include <algorithm>
#include <iomanip>

Expand Down Expand Up @@ -54,14 +53,7 @@ void MD_base::setup(ModuleESolver::ESolver* p_esolver, const std::string& global
restart(global_readin_dir);
}

// mohan add 2026-01-04
const int stress_step = 0;
const int force_step = 0;
const int istep_print = step_ + step_rst_ + 1;

ModuleIO::print_screen(stress_step, force_step, istep_print);

MD_func::force_virial(p_esolver, step_, mdcell, decomp, potential, cal_stress, virial, mdp.md_out_force);
MD_func::force_virial(p_esolver, step_, mdcell, decomp, potential, cal_stress, virial);
MD_func::compute_stress(mdcell, cal_stress, virial, stress);
if (mdcell.has_backing_unitcell())
{
Expand Down
7 changes: 1 addition & 6 deletions source/source_md/md_func.cpp
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Expand Up @@ -329,8 +329,7 @@ void force_virial(ModuleESolver::ESolver* p_esolver,
DomainDecomposition& decomp,
double& potential,
const bool& cal_stress,
ModuleBase::matrix& virial,
const bool& md_out_force)
ModuleBase::matrix& virial)
{
ModuleBase::TITLE("MD_func", "force_virial");
ModuleBase::timer::start("MD_func", "force_virial");
Expand All @@ -341,10 +340,6 @@ void force_virial(ModuleESolver::ESolver* p_esolver,
decomp.accumulate_ghost_forces(mdcell);
potential = 0.5 * p_esolver->cal_energy();
for (LocalAtom& atom : mdcell.owned_atoms()) atom.force *= 0.5;
if (md_out_force)
{
ModuleIO::print_force(GlobalV::ofs_running, mdcell, "TOTAL-FORCE (eV/Angstrom)");
}
if (cal_stress) { p_esolver->cal_stress(static_cast<BaseCell&>(mdcell), virial); virial *= 0.5; }
}
else
Expand Down
3 changes: 1 addition & 2 deletions source/source_md/md_func.h
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Expand Up @@ -95,8 +95,7 @@ void force_virial(ModuleESolver::ESolver* p_esolver,
DomainDecomposition& decomp,
double& potential,
const bool& cal_stress,
ModuleBase::matrix& virial,
const bool& md_out_force);
ModuleBase::matrix& virial);
/**
* @brief calculate the ionic kinetic energy
*
Expand Down
33 changes: 28 additions & 5 deletions source/source_md/run_md.cpp
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Expand Up @@ -191,6 +191,10 @@ void md_line(MDCell& mdcell,
/// md cycle, mohan update 2026-01-04, change '<=' to '<'
while ((mdrun->step_ + mdrun->step_rst_) < param_in.mdp.md_nstep && !mdrun->stop)
{
int md_step = mdrun->step_ + mdrun->step_rst_;
int thermo_step = mdrun->step_ == 0 ? md_step : md_step + 1;

@Critsium-xy Critsium-xy Oct 26, 2026

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The gating index is inconsistent: step 0 is tested with the 0-based md_step, later steps with md_step + 1.

  • With md_thermo_freq=10, thermo is printed at steps 0, 9, 19, 29, ..., while md_dumpfreq/md_restartfreq use md_step % freq (0, 10, 20, ...), so thermo records do not line up with MD_dump frames.
  • On restart from step_rst_=10, the first resumed step is tested with 10 (printed), whereas the same step in an uninterrupted run is tested with 11 (not printed); output depends on whether the run was restarted.

Suggest using md_step % md_thermo_freq == 0 uniformly, consistent with the other MD frequencies.

bool print_thermo = param_in.mdp.md_thermo_freq > 0
&& thermo_step % param_in.mdp.md_thermo_freq == 0;
#ifdef __JSON
// JSON output currently follows the UnitCell-backed electronic-structure path.
// Start one output record before the solver appends SCF information for this MD step.
Expand All @@ -204,6 +208,20 @@ void md_line(MDCell& mdcell,
{
mdrun->setup(p_esolver, param_in.globalv.global_readin_dir, decomp);

// setup() may load step_rst_ from Restart_md.txt.
md_step = mdrun->step_ + mdrun->step_rst_;
thermo_step = md_step;
print_thermo = param_in.mdp.md_thermo_freq > 0
&& thermo_step % param_in.mdp.md_thermo_freq == 0;

if (print_thermo)

@Critsium-xy Critsium-xy Oct 26, 2026 •
edited
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Ordering regression: MD_base::setup() used to print the step banner before force_virial(); now it is printed after setup() returns, so for DFT MD the first step's SCF output precedes STEP OF MOLECULAR DYNAMICS: 1. Minimal fix: keep print_screen at its original place in setup() (after restart()) and gate it with mdp.md_thermo_freq > 0 && (step_ + step_rst_) % mdp.md_thermo_freq == 0; mdp is already a member, and the recomputation block here can then be dropped.

{
const int stress_step = 0;
const int force_step = 0;
const int istep_print = md_step + 1;
ModuleIO::print_screen(stress_step, force_step, istep_print);
}

if (param_in.mdp.plumed)
{
int nproc = 1;
Expand Down Expand Up @@ -235,8 +253,11 @@ void md_line(MDCell& mdcell,
// mohan add 2026-01-04
const int stress_step = 0;
const int force_step = 0;
const int istep_print = mdrun->step_ + mdrun->step_rst_ + 1;
ModuleIO::print_screen(stress_step, force_step, istep_print);
const int istep_print = thermo_step;
if (print_thermo)
{
ModuleIO::print_screen(stress_step, force_step, istep_print);
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}
mdrun->first_half(GlobalV::ofs_running);

/// update force and virial due to the update of atom positions
Expand All @@ -246,8 +267,7 @@ void md_line(MDCell& mdcell,
decomp,
mdrun->potential,
param_in.inp.cal_stress,
mdrun->virial,
param_in.mdp.md_out_force);
mdrun->virial);

if (plumed.active())
{
Expand All @@ -268,7 +288,10 @@ void md_line(MDCell& mdcell,
mdrun->frozen_freedom_);
}

mdrun->print_md(GlobalV::ofs_running, PARAM.inp.cal_stress);
if (print_thermo)
{
mdrun->print_md(GlobalV::ofs_running, param_in.inp.cal_stress);
}
if (param_in.mdp.md_dumpfreq > 0
&& (mdrun->step_ + mdrun->step_rst_) % param_in.mdp.md_dumpfreq == 0)
{
Expand Down
6 changes: 3 additions & 3 deletions source/source_md/test/lj_pot_test.cpp
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Expand Up @@ -48,7 +48,7 @@ TEST_F(LJ_pot_test, potential)
DomainDecomposition decomp;
decomp.init(ModuleBase::world_comm_domain(), mdcell.latvec(), mdcell.lat0(), 0.0, 0.0);
p_esolver->before_all_runners(mdcell, inp);
MD_func::force_virial(p_esolver, 0, mdcell, decomp, potential, true, stress, false);
MD_func::force_virial(p_esolver, 0, mdcell, decomp, potential, true, stress);
EXPECT_NEAR(potential, -0.011957818623534381, doublethreshold);
}

Expand All @@ -73,7 +73,7 @@ TEST_F(LJ_pot_test, force)
DomainDecomposition decomp;
decomp.init(ModuleBase::world_comm_domain(), mdcell.latvec(), mdcell.lat0(), 0.0, 0.0);
p_esolver->before_all_runners(mdcell, inp);
MD_func::force_virial(p_esolver, 0, mdcell, decomp, potential, true, stress, false);
MD_func::force_virial(p_esolver, 0, mdcell, decomp, potential, true, stress);
const std::vector<LocalAtom>& atoms = mdcell.owned_atoms();
EXPECT_NEAR(atoms[0].force.x, 0.00049817733089377704, doublethreshold);
EXPECT_NEAR(atoms[0].force.y, 0.00082237246837022328, doublethreshold);
Expand Down Expand Up @@ -119,7 +119,7 @@ TEST_F(LJ_pot_test, stress)
DomainDecomposition decomp;
decomp.init(ModuleBase::world_comm_domain(), mdcell.latvec(), mdcell.lat0(), 0.0, 0.0);
p_esolver->before_all_runners(mdcell, inp);
MD_func::force_virial(p_esolver, 0, mdcell, decomp, potential, true, stress, false);
MD_func::force_virial(p_esolver, 0, mdcell, decomp, potential, true, stress);
EXPECT_NEAR(stress(0, 0), 8.0360222227631859e-07, doublethreshold);
EXPECT_NEAR(stress(0, 1), 1.7207745586539077e-07, doublethreshold);
EXPECT_NEAR(stress(0, 2), 0.0, doublethreshold);
Expand Down
2 changes: 1 addition & 1 deletion source/source_md/test/test_md_func.cpp
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Expand Up @@ -64,7 +64,7 @@ TEST(MdForceVirialTest, ReturnsGhostForcesBeforeConvertingUnitsExactlyOnce)
ModuleBase::matrix virial(3, 3);
for (int step = 0; step < 2; ++step)
{
MD_func::force_virial(&solver, step, cell, decomp, potential, true, virial, false);
MD_func::force_virial(&solver, step, cell, decomp, potential, true, virial);
EXPECT_DOUBLE_EQ(potential, 3.0);
EXPECT_DOUBLE_EQ(virial(0, 0), 4.0);
ASSERT_EQ(cell.owned_atoms().size(), 1);
Expand Down
2 changes: 1 addition & 1 deletion tests/07_OFDFT/25_OF_MD_LDA/INPUT
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Expand Up @@ -27,7 +27,7 @@ md_type nvt
md_nstep 3
md_dt 0.25
md_tfirst 58022.52706
md_dumpfreq 10
md_dumpfreq 1
md_tfreq 1.08
md_tchain 1
nbspline 10 # be sure fft dimension is odd
2 changes: 1 addition & 1 deletion tests/07_OFDFT/26_OF_MD_LibxcPBE/INPUT
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Expand Up @@ -27,7 +27,7 @@ md_type nvt
md_nstep 3
md_dt 0.25
md_tfirst 58022.52706
md_dumpfreq 10
md_dumpfreq 1
md_tfreq 1.08
md_tchain 1
nbspline 10 # be sure fft dimension is odd
Expand Down
2 changes: 1 addition & 1 deletion tests/07_OFDFT/30_TDOFDFT_Al/INPUT
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Expand Up @@ -30,7 +30,7 @@ md_type nve
md_nstep 3
md_dt 0.25
md_tfirst 58022.52706
md_dumpfreq 10
md_dumpfreq 1
md_tfreq 1.08
md_tchain 1
nbspline 10 # be sure fft dimension is odd
2 changes: 1 addition & 1 deletion tests/07_OFDFT/31_TDOFDFT_Al_CD/INPUT
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Expand Up @@ -31,7 +31,7 @@ md_type nve
md_nstep 3
md_dt 0.25
md_tfirst 58022.52706
md_dumpfreq 10
md_dumpfreq 1
md_tfreq 1.08
md_tchain 1
nbspline 10 # be sure fft dimension is odd
2 changes: 1 addition & 1 deletion tests/07_OFDFT/32_TDOFDFT_Al_mCD/INPUT
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Expand Up @@ -31,7 +31,7 @@ md_type nve
md_nstep 3
md_dt 0.25
md_tfirst 58022.52706
md_dumpfreq 10
md_dumpfreq 1
md_tfreq 1.08
md_tchain 1
nbspline 10 # be sure fft dimension is odd
2 changes: 1 addition & 1 deletion tests/integrate/validation_tools/catch_properties.sh
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Expand Up @@ -26,7 +26,7 @@ source "$PROPS_SCRIPT_DIR/props_deepks.sh"
# trailing totaltimeref entry. Add a new category by dropping a
# props_<cat>.sh next to the others and calling run_<cat>_props here.
run_lr_force_props
run_basic_props
run_basic_props || exit 1

#-------------------------------
# matrix collectors: out_dm1 (props_mat.sh)
Expand Down
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