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Refactor implicit solvation model #6836

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Merged
mohanchen merged 3 commits into from
Jan 7, 2026
Merged

Refactor implicit solvation model #6836

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32b673d
sol refactor
LKFEIYI Jan 6, 2026
9256a90
remove unused variable
LKFEIYI Jan 7, 2026
c640326
Clean up comments in cal_vcav.cpp
LKFEIYI Jan 7, 2026
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19 changes: 11 additions & 8 deletions source/source_estate/module_pot/pot_surchem.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -31,21 +31,24 @@ class PotSurChem : public PotBase
}
}

// Passing an explicit output matrix makes the lifetime and allocation explicit and avoids hidden allocations.
void cal_v_eff(const Charge*const chg, const UnitCell*const ucell, ModuleBase::matrix& v_eff) override
{
if (!this->allocated)
{
this->surchem_->allocate(this->rho_basis_->nrxx, v_eff.nr);
this->allocated = true;
}

v_eff += this->surchem_->v_correction(*ucell,
*chg->pgrid,
const_cast<ModulePW::PW_Basis*>(this->rho_basis_),
v_eff.nr,
chg->rho,
this->vlocal,
this->structure_factors_);
ModuleBase::matrix v_sol_correction(v_eff.nr, this->rho_basis_->nrxx);
this->surchem_->v_correction(*ucell,
*chg->pgrid,
const_cast<ModulePW::PW_Basis*>(this->rho_basis_),
v_eff.nr,
chg->rho,
this->vlocal,
this->structure_factors_,
v_sol_correction);
v_eff += v_sol_correction;
}

private:
Expand Down
32 changes: 19 additions & 13 deletions source/source_hamilt/module_surchem/H_correction_pw.cpp
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Expand Up @@ -5,14 +5,15 @@
#include "source_base/timer.h"
#include "source_hamilt/module_xc/xc_functional.h"
#include "surchem.h"

ModuleBase::matrix surchem::v_correction(const UnitCell& cell,
const Parallel_Grid& pgrid,
const ModulePW::PW_Basis* rho_basis,
const int& nspin,
const double* const* const rho,
const double* vlocal,
Structure_Factor* sf)
// Changing the interface to use an explicit output parameter clarifies lifetime management and avoids hidden allocations.
void surchem::v_correction(const UnitCell& cell,
const Parallel_Grid& pgrid,
const ModulePW::PW_Basis* rho_basis,
const int& nspin,
const double* const* const rho,
const double* vlocal,
Structure_Factor* sf,
ModuleBase::matrix& v)
{
ModuleBase::TITLE("surchem", "v_cor");
ModuleBase::timer::tick("surchem", "v_cor");
Expand Down Expand Up @@ -46,10 +47,15 @@ ModuleBase::matrix surchem::v_correction(const UnitCell& cell,

cal_pseudo(cell, pgrid, rho_basis, porter_g, ps_totn, sf);

ModuleBase::matrix v(nspin, rho_basis->nrxx);
// ModuleBase::matrix v(nspin, rho_basis->nrxx);
if (v.nr != nspin || v.nc != rho_basis->nrxx)
{
v.create(nspin, rho_basis->nrxx);
}
ModuleBase::GlobalFunc::ZEROS(v.c, nspin * rho_basis->nrxx);

v += cal_vel(cell, rho_basis, total_n, ps_totn, nspin);
v += cal_vcav(cell, rho_basis, ps_totn, nspin);
cal_vel(cell, rho_basis, total_n, ps_totn, nspin, v);
cal_vcav(cell, rho_basis, ps_totn, nspin, v);

delete[] porter;
delete[] porter_g;
Expand All @@ -58,5 +64,5 @@ ModuleBase::matrix surchem::v_correction(const UnitCell& cell,
delete[] total_n;

ModuleBase::timer::tick("surchem", "v_cor");
return v;
}
return;
}
4 changes: 2 additions & 2 deletions source/source_hamilt/module_surchem/cal_pseudo.cpp
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Expand Up @@ -9,8 +9,8 @@ void surchem::gauss_charge(const UnitCell& cell,
std::complex<double>* N,
Structure_Factor* sf)
{
sf->setup(&cell, pgrid, rho_basis); // this is strange, should be removed to other places, mohan add 2025-11-04

//sf->setup(&cell, pgrid, rho_basis); // this is strange, should be removed to other places, mohan add 2025-11-04
//sf here was only needed in the test.
const int ig0 = rho_basis->ig_gge0; // G=0 index
for (int it = 0; it < cell.ntype; it++)
{
Expand Down
38 changes: 22 additions & 16 deletions source/source_hamilt/module_surchem/cal_vcav.cpp
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Expand Up @@ -16,25 +16,26 @@ void lapl_rho(const double& tpiba2,
// the formula is : rho(r)^prime = \int iG * rho(G)e^{iGr} dG
for (int ig = 0; ig < rho_basis->npw; ig++) {
gdrtmpg[ig] = rhog[ig];
}
}

for(int i = 0 ; i < 3 ; ++i)
{
// calculate the charge density gradient in reciprocal space.
// calculate the charge density gradient in reciprocal space.
for (int ig = 0; ig < rho_basis->npw; ig++) {
aux[ig] = gdrtmpg[ig] * pow(rho_basis->gcar[ig][i], 2);
}
}

// bring the gdr from G --> R
rho_basis->recip2real(aux, aux);

// remember to multily 2pi/a0, which belongs to G vectors.
for (int ir = 0; ir < rho_basis->nrxx; ir++) {
lapn[ir] -= aux[ir].real() * tpiba2;
}

}
}

delete[] gdrtmpg;
delete[] aux;
return;
}

// calculates first derivative of the shape function in realspace
Expand Down Expand Up @@ -66,6 +67,7 @@ void surchem::createcavity(const UnitCell& ucell,
{
ModuleBase::Vector3<double> *nablan = new ModuleBase::Vector3<double>[rho_basis->nrxx];
ModuleBase::GlobalFunc::ZEROS(nablan, rho_basis->nrxx);

double *nablan_2 = new double[rho_basis->nrxx];
double *sqrt_nablan_2 = new double[rho_basis->nrxx];
double *lapn = new double[rho_basis->nrxx];
Expand All @@ -77,14 +79,14 @@ void surchem::createcavity(const UnitCell& ucell,
// nabla n
XC_Functional::grad_rho(ps_totn, nablan, rho_basis, ucell.tpiba);

// |\nabla n |^2 = nablan_2
// |\nabla n |^2 = nablan_2
for (int ir = 0; ir < rho_basis->nrxx; ir++)
{
nablan_2[ir] = pow(nablan[ir].x, 2) + pow(nablan[ir].y, 2) + pow(nablan[ir].z, 2);
}

// Laplacian of n
lapl_rho(ucell.tpiba2,ps_totn, lapn, rho_basis);
lapl_rho(ucell.tpiba2, ps_totn, lapn, rho_basis);

//-------------------------------------------------------------
// add -Lap(n)/|\nabla n| to vwork and copy \sqrt(|\nabla n|^2)
Expand Down Expand Up @@ -162,10 +164,13 @@ void surchem::createcavity(const UnitCell& ucell,
delete[] ggn;
}

ModuleBase::matrix surchem::cal_vcav(const UnitCell& ucell,
const ModulePW::PW_Basis* rho_basis,
std::complex<double>* ps_totn,
int nspin)
//The interface is changed to use an explicit output parameter to
//clarify lifetime management and avoid hidden allocations.
void surchem::cal_vcav(const UnitCell& ucell,
const ModulePW::PW_Basis* rho_basis,
std::complex<double>* ps_totn,
int nspin,
ModuleBase::matrix& v)
{
ModuleBase::TITLE("surchem", "cal_vcav");
ModuleBase::timer::tick("surchem", "cal_vcav");
Expand All @@ -175,12 +180,12 @@ ModuleBase::matrix surchem::cal_vcav(const UnitCell& ucell,

createcavity(ucell, rho_basis, ps_totn, tmp_Vcav);

ModuleBase::GlobalFunc::ZEROS(Vcav.c, nspin * rho_basis->nrxx);
if (nspin == 4)
{
for (int ir = 0; ir < rho_basis->nrxx; ir++)
{
Vcav(0, ir) += tmp_Vcav[ir];
Vcav(0, ir) = tmp_Vcav[ir];
v(0, ir) += Vcav(0, ir);
}
}
else
Expand All @@ -189,12 +194,13 @@ ModuleBase::matrix surchem::cal_vcav(const UnitCell& ucell,
{
for (int ir = 0; ir < rho_basis->nrxx; ir++)
{
Vcav(is, ir) += tmp_Vcav[ir];
Vcav(is, ir) = tmp_Vcav[ir];
v(is, ir) += Vcav(is, ir);
}
}
}

delete[] tmp_Vcav;
ModuleBase::timer::tick("surchem", "cal_vcav");
return Vcav;
return;
}
19 changes: 12 additions & 7 deletions source/source_hamilt/module_surchem/cal_vel.cpp
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Expand Up @@ -54,11 +54,14 @@ void eps_pot(const double* PS_TOTN_real,
delete[] phisq;
}

ModuleBase::matrix surchem::cal_vel(const UnitCell& cell,
const ModulePW::PW_Basis* rho_basis,
std::complex<double>* TOTN,
std::complex<double>* PS_TOTN,
int nspin)
//The interface is changed to use an explicit output parameter to
//clarify lifetime management and avoid hidden allocations.
void surchem::cal_vel(const UnitCell& cell,
const ModulePW::PW_Basis* rho_basis,
std::complex<double>* TOTN,
std::complex<double>* PS_TOTN,
int nspin,
ModuleBase::matrix& v)
{
ModuleBase::TITLE("surchem", "cal_vel");
ModuleBase::timer::tick("surchem", "cal_vel");
Expand Down Expand Up @@ -134,6 +137,7 @@ ModuleBase::matrix surchem::cal_vel(const UnitCell& cell,
for (int ir = 0; ir < rho_basis->nrxx; ir++)
{
Vel(0, ir) += tmp_Vel[ir];
v(0, ir) += Vel(0, ir);
}
}
else
Expand All @@ -143,6 +147,7 @@ ModuleBase::matrix surchem::cal_vel(const UnitCell& cell,
for (int ir = 0; ir < rho_basis->nrxx; ir++)
{
Vel(is, ir) += tmp_Vel[ir];
v(is, ir) += Vel(is, ir);
}
}
}
Expand All @@ -158,5 +163,5 @@ ModuleBase::matrix surchem::cal_vel(const UnitCell& cell,
delete[] phi_tilda_R0;

ModuleBase::timer::tick("surchem", "cal_vel");
return Vel;
}
return;
}
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