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Fixed one obvious error in numdiff version, matching analytic quite well for P~=0, need to fix addon term

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This commit is contained in:
Aidan Thompson
2022-02-03 17:44:47 -07:00
parent b7c8ab639c
commit 7cd9975e29
4 changed files with 65 additions and 26 deletions
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64
src/EXTRA-COMPUTE/compute_born_matrix.cpp
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@ -287,7 +287,8 @@ void ComputeBornMatrix::init()
// to convert to vector indexing:
// matrix index to vector index, double -> single index
// this is not used at all
voigt3MtoV[0][0]=0; voigt3MtoV[0][1]=5; voigt3MtoV[0][2]=4;
voigt3MtoV[1][0]=5; voigt3MtoV[1][1]=1; voigt3MtoV[1][2]=3;
voigt3MtoV[2][0]=4; voigt3MtoV[2][1]=3; voigt3MtoV[2][2]=2;
@ -299,8 +300,19 @@ void ComputeBornMatrix::init()
virialMtoV[0][0]=0; virialMtoV[0][1]=3; virialMtoV[0][2]=4;
virialMtoV[1][0]=3; virialMtoV[1][1]=1; virialMtoV[1][2]=5;
virialMtoV[2][0]=4; virialMtoV[2][1]=5; virialMtoV[2][2]=2;
// the following is for 6x6 matrix and vector indexing converter
// reorder LAMMPS virial vector to Voigt order
virialVtoV[0] = 0;
virialVtoV[1] = 1;
virialVtoV[2] = 2;
virialVtoV[3] = 5;
virialVtoV[4] = 4;
virialVtoV[5] = 3;
// the following is for 6x6 matrix and vector indexing converter // this is clearly different order form albe[][] and revalbe[]
// should not be used
int indcounter = 0;
for(int row = 0; row < NDIR_VIRIAL; row++)
for(int col = row; col< NDIR_VIRIAL; col++) {
@ -351,6 +363,13 @@ void ComputeBornMatrix::compute_vector()
MPI_Allreduce(values_local, values_global, nvalues, MPI_DOUBLE, MPI_SUM, world);
// convert to pressure units
double nktv2p = force->nktv2p;
double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
for (int m = 0; m < nvalues; m++) { values_global[m] *=
(nktv2p * inv_volume); }
} else {
// calculate Born matrix using stress finite differences
@ -358,9 +377,9 @@ void ComputeBornMatrix::compute_vector()
compute_numdiff();
}
for (int m = 0; m < nvalues; m++) { vector[m] = values_global[m]; }
for (int m = 0; m < nvalues; m++) vector[m] = values_global[m];
}
/* ----------------------------------------------------------------------
@ -443,7 +462,8 @@ void ComputeBornMatrix::compute_pairs()
// Add contribution to Born tensor
pair->born_matrix(i, j, itype, jtype, rsq, factor_coul, factor_lj, dupair, du2pair);
pair_pref = du2pair - dupair * rinv;
// pair_pref = du2pair - dupair * rinv;
pair_pref = du2pair;
// See albemunu in compute_born_matrix.h for indices order.
@ -489,7 +509,7 @@ void ComputeBornMatrix::compute_numdiff()
}
// loop over 6 strain directions
// compute a finite difference force in each dimension
// compute stress finite difference in each direction
int flag, allflag;
@ -499,26 +519,24 @@ void ComputeBornMatrix::compute_numdiff()
update_virial();
for (int jdir = 0; jdir < NDIR_VIRIAL; jdir++) {
m = revalbe[idir][jdir];
values_global[m] = compute_virial->vector[jdir];
values_global[m] = compute_virial->vector[virialVtoV[jdir]];
}
restore_atoms(nall, idir);
displace_atoms(nall, idir, -1.0);
force_clear(nall);
update_virial();
for (int jdir = 0; jdir < NDIR_VIRIAL; jdir++) {
m = revalbe[idir][jdir];
values_global[m] -= compute_virial->vector[jdir];
values_global[m] -= compute_virial->vector[virialVtoV[jdir]];
}
restore_atoms(nall, idir);
}
// apply derivative factor
double nktv2p = force->nktv2p;
double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
// double denominator = -0.5 / numdelta * inv_volume * nktv2p;
double denominator = -0.5 / numdelta;
for (int m = 0; m < nvalues; m++) values_global[m] *= denominator;
// recompute virial so all virial and energy contributions are as before
// also needed for virial stress addon contributions to Born matrix
@ -526,15 +544,14 @@ void ComputeBornMatrix::compute_numdiff()
update_virial();
// virial_addon();
// restore original forces for owned and ghost atoms
for (int i = 0; i < nall; i++)
for (int k = 0; k < 3; k++)
f[i][k] = temp_f[i][k];
for (int m = 0; m < nvalues; m++) values_global[m] *= denominator;
virial_addon();
}
/* ----------------------------------------------------------------------
@ -544,6 +561,7 @@ void ComputeBornMatrix::compute_numdiff()
void ComputeBornMatrix::displace_atoms(int nall, int idir, double magnitude)
{
double **x = atom->x;
int k = dirlist[idir][0];
int l = dirlist[idir][1];
for (int i = 0; i < nall; i++)
@ -556,9 +574,13 @@ void ComputeBornMatrix::displace_atoms(int nall, int idir, double magnitude)
void ComputeBornMatrix::restore_atoms(int nall, int idir)
{
// reset all coords, just to be safe, ignore idir
double **x = atom->x;
int k = dirlist[idir][0];
for (int i = 0; i < nall; i++) { x[i][k] = temp_x[i][k]; }
for (int i = 0; i < nall; i++)
for (int k = 0; k < 3; k++)
x[i][k] = temp_x[i][k];
}
/* ----------------------------------------------------------------------
@ -585,7 +607,6 @@ void ComputeBornMatrix::update_virial()
compute_virial->compute_vector();
}
/* ----------------------------------------------------------------------
calculate virial stress addon terms to the Born matrix
this is based on original code of Dr. Yubao Zhen
@ -630,7 +651,8 @@ void ComputeBornMatrix::virial_addon()
if(SHEAR)
addon += kronecker[jd][nd]*sigv[virialMtoV[id][kd]] +
kronecker[jd][kd]*sigv[virialMtoV[id][nd]];
values_global[voigt6MtoV[ijvgt][knvgt]] += addon;
// values_global[voigt6MtoV[ijvgt][knvgt]] += addon;
values_global[revalbe[ijvgt][knvgt]] += addon;
}
}
}