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USER-BOCS and other compute pressures

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This commit is contained in:
Plimpton
2021-01-21 17:27:45 -07:00
parent 5a23b804d9
commit d169f6c169
3 changed files with 21 additions and 19 deletions
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23
src/USER-BOCS/compute_pressure_bocs.cpp
View File

@ -158,9 +158,12 @@ void ComputePressureBocs::init()
if (dihedralflag && force->dihedral) nvirial++;
if (improperflag && force->improper) nvirial++;
}
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_flag) nvirial++;
if (fixflag) {
Fix **fix = modify->fix;
int nfix = modify->nfix;
for (int i = 0; i < nfix; i++)
if (fix[i]->thermo_virial) nvirial++;
}
if (nvirial) {
vptr = new double*[nvirial];
@ -174,7 +177,7 @@ void ComputePressureBocs::init()
vptr[nvirial++] = force->improper->virial;
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_flag)
if (modify->fix[i]->virial_global_flag && modify->fix[i]->thermo_virial)
vptr[nvirial++] = modify->fix[i]->virial;
}
@ -184,26 +187,24 @@ void ComputePressureBocs::init()
else kspace_virial = nullptr;
}
/* Extra functions added for BOCS */
/* ----------------------------------------------------------------------
Compute the pressure correction for the analytical basis set
------------------------------------------------------------------------- */
double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff,
int N_mol, double vavg, double vCG)
{
double correction = 0.0;
for (int i = 1; i <= N_basis; ++i)
{
correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) *
pow( ( 1 / vavg ) * ( vCG - vavg ),i-1);
}
return correction;
}
/* ----------------------------------------------------------------------
Find the relevant index position if using a spline basis set
------------------------------------------------------------------------- */
double ComputePressureBocs::find_index(double * grid, double value)
{
int i;
@ -256,8 +257,10 @@ double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
send cg info from fix_bocs to compute_pressure_bocs for the analytical
basis set
------------------------------------------------------------------------- */
void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
double *sent_phi_coeff, int sent_N_mol, double sent_vavg)
double *sent_phi_coeff, int sent_N_mol,
double sent_vavg)
{
if (basis_type == BASIS_ANALYTIC) { p_basis_type = BASIS_ANALYTIC; }
else
@ -280,6 +283,7 @@ void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
send cg info from fix_bocs to compute_pressure_bocs for a spline basis
set
------------------------------------------------------------------------- */
void ComputePressureBocs::send_cg_info(int basis_type,
double ** in_splines, int gridsize)
{
@ -299,6 +303,7 @@ void ComputePressureBocs::send_cg_info(int basis_type,
/* ----------------------------------------------------------------------
compute total pressure, averaged over Pxx, Pyy, Pzz
------------------------------------------------------------------------- */
double ComputePressureBocs::compute_scalar()
{
invoked_scalar = update->ntimestep;

9
src/compute_pressure.cpp
View File

@ -215,14 +215,11 @@ void ComputePressure::init()
vptr[nvirial++] = force->dihedral->virial;
if (improperflag && force->improper)
vptr[nvirial++] = force->improper->virial;
if (fixflag) {
Fix **fix = modify->fix;
int nfix = modify->nfix;
for (int i = 0; i < nfix; i++)
if (fix[i]->virial_global_flag && fix[i]->thermo_virial)
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_global_flag && modify->fix[i]->thermo_virial)
vptr[nvirial++] = modify->fix[i]->virial;
}
}
// flag Kspace contribution separately, since not summed across procs

2
src/compute_stress_atom.cpp
View File

@ -223,7 +223,7 @@ void ComputeStressAtom::compute_peratom()
int nfix = modify->nfix;
for (int ifix = 0; ifix < nfix; ifix++)
if (fix[i]->virial_peratom_flag && fix[ifix]->thermo_virial) {
double **vatom = modify->fix[ifix]->vatom;
double **vatom = fix[ifix]->vatom;
if (vatom)
for (i = 0; i < nlocal; i++)
for (j = 0; j < 6; j++)