ICODE-ADC/lammps
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rename some function & variable, output delta area

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This commit is contained in:
davidfir3
2022-03-27 20:52:00 +08:00
parent 7c333b8e07
commit 603136a93b
2 changed files with 13 additions and 12 deletions
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23
src/FEP/compute_fep_ta.cpp
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@ -52,7 +52,7 @@ ComputeFEPTA::ComputeFEPTA(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 0;
vector_flag = 1;
size_vector = 2;
size_vector = 3;
extvector = 0;
vector = new double[size_vector];
@ -90,7 +90,7 @@ ComputeFEPTA::ComputeFEPTA(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal optional keyword in compute fep/ta");
}
// allocate space for position, charge, force, energy, virial arrays
// allocate space for position, force, energy, virial arrays
x_orig = nullptr;
f_orig = nullptr;
@ -171,7 +171,7 @@ void ComputeFEPTA::compute_vector()
backup_xfev(); // backup position, force, energy, virial array values
backup_box(); // backup box size
pe0 = compute_epair();
pe0 = compute_pe();
change_box();
comm->forward_comm();
@ -200,7 +200,7 @@ void ComputeFEPTA::compute_vector()
// otherwise the force compute on the GPU in the next step would be incorrect
if (fixgpu) fixgpu->post_force(vflag);
pe1 = compute_epair();
pe1 = compute_pe();
restore_xfev(); // restore position, force, energy, virial array values
restore_box(); // restore box size
@ -208,16 +208,17 @@ void ComputeFEPTA::compute_vector()
vector[0] = pe1-pe0;
vector[1] = exp(-(pe1-pe0)/(force->boltz*temp_fep));
vector[2] = area_orig*(scale_factor-1.0);
}
/* ----------------------------------------------------------------------
obtain pair energy from lammps accumulators
obtain potential energy from lammps accumulators
------------------------------------------------------------------------- */
double ComputeFEPTA::compute_epair()
double ComputeFEPTA::compute_pe()
{
double eng, eng_pair;
double eng, eng_potential;
eng = 0.0;
if (force->pair)
@ -230,16 +231,16 @@ double ComputeFEPTA::compute_epair()
if (force->improper) eng += force->improper->energy;
}
MPI_Allreduce(&eng,&eng_pair,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&eng,&eng_potential,1,MPI_DOUBLE,MPI_SUM,world);
if (tailflag) {
double volume = domain->xprd * domain->yprd * domain->zprd;
eng_pair += force->pair->etail / volume;
eng_potential += force->pair->etail / volume;
}
if (force->kspace) eng_pair += force->kspace->energy;
if (force->kspace) eng_potential += force->kspace->energy;
return eng_pair;
return eng_potential;
}

2
src/FEP/compute_fep_ta.h
View File

@ -59,7 +59,7 @@ class ComputeFEPTA : public Compute {
class Fix *fixgpu;
double compute_epair();
double compute_pe();
void change_box();
void backup_box();
void restore_box();