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Hopefully got compute_born_matrix numdiff method working. Also added two BORN_MATRIX examples.

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This commit is contained in:
Germain Clavier
2022-02-08 16:40:52 +01:00
parent ba89ad546a
commit 9833e5bc66
19 changed files with 200696 additions and 38 deletions
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100
src/EXTRA-COMPUTE/compute_born_matrix.cpp
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@ -165,48 +165,59 @@ ComputeBornMatrix::ComputeBornMatrix(LAMMPS *lmp, int narg, char **arg) :
}
if (pairflag) {
if (numflag) error->all(FLERR, "Illegal compute born/matrix command");
if (numflag) error->all(FLERR, "Illegal compute born/matrix command: cannot mix numflag and other flags");
if (force->pair) {
if (force->pair->born_matrix_enable == 0) {
if (comm->me == 0) error->warning(FLERR, "Pair style does not support compute born/matrix");
}
} else {
pairflag = 0;
}
}
if (bondflag) {
if (numflag) error->all(FLERR, "Illegal compute born/matrix command");
if (numflag) error->all(FLERR, "Illegal compute born/matrix command: cannot mix numflag and other flags");
if (force->bond) {
if (force->bond->born_matrix_enable == 0) {
if (comm->me == 0) error->warning(FLERR, "Bond style does not support compute born/matrix");
}
} else {
bondflag = 0;
}
}
if (angleflag) {
if (numflag) error->all(FLERR, "Illegal compute born/matrix command");
if (numflag) error->all(FLERR, "Illegal compute born/matrix command: cannot mix numflag and other flags");
if (force->angle) {
if (force->angle->born_matrix_enable == 0) {
if (comm->me == 0) error->warning(FLERR, "Angle style does not support compute born/matrix");
}
} else {
angleflag = 0;
}
}
if (dihedflag) {
if (numflag) error->all(FLERR, "Illegal compute born/matrix command");
if (numflag) error->all(FLERR, "Illegal compute born/matrix command: cannot mix numflag and other flags");
if (force->dihedral) {
if (force->dihedral->born_matrix_enable == 0) {
if (comm->me == 0) error->warning(FLERR, "Dihedral style does not support compute born/matrix");
}
} else {
dihedflag = 0;
}
}
if (impflag) {
if (numflag) error->all(FLERR, "Illegal compute born/matrix command");
if (numflag) error->all(FLERR, "Illegal compute born/matrix command: cannot mix numflag and other flags");
if (force->improper) {
if (force->improper->born_matrix_enable == 0) {
if (comm->me == 0) error->warning(FLERR, "Improper style does not support compute born/matrix");
}
} else {
impflag = 0;
}
}
if (force->kspace) {
if (!numflag) error->warning(FLERR, "KSPACE contribution not supported by compute born/matrix");
}
// Initialize some variables
values_local = values_global = vector = nullptr;
@ -292,18 +303,18 @@ void ComputeBornMatrix::init()
// set up reverse index lookup
for (int m = 0; m < nvalues; m++) {
int a = albe[m][0];
int b = albe[m][1];
int a = C_albe[m][0];
int b = C_albe[m][1];
revalbe[a][b] = m;
revalbe[b][a] = m;
}
for (int a = 0; a < NDIR_VIRIAL; a++) {
for (int b = 0; b < NDIR_VIRIAL; b++) {
printf("%d ",revalbe[a][b]);
}
printf("\n");
}
// for (int a = 0; a < NDIR_VIRIAL; a++) {
// for (int b = 0; b < NDIR_VIRIAL; b++) {
// printf("%d ",revalbe[a][b]);
// }
// printf("\n");
// }
// voigt3VtoM notation in normal physics sense,
// 3x3 matrix and vector indexing
@ -358,6 +369,13 @@ void ComputeBornMatrix::init()
voigt6MtoV[row][col] = voigt6MtoV[col][row] = indcounter;
indcounter++;
}
// printf("Voigt6MtoV:\n");
// for (int a = 0; a < NDIR_VIRIAL; a++) {
// for (int b = 0; b < NDIR_VIRIAL; b++) {
// printf("%d ", voigt6MtoV[a][b]);
// }
// printf("\n");
// }
// set up 3x3 kronecker deltas
@ -415,6 +433,13 @@ void ComputeBornMatrix::compute_vector()
// calculate Born matrix using stress finite differences
compute_numdiff();
// for consistency this is returned in energy units
double inv_nktv2p = 1.0/force->nktv2p;
double volume = domain->xprd * domain->yprd * domain->zprd;
for (int m = 0; m < nvalues; m++) {
values_global[m] *= inv_nktv2p * volume;
}
}
for (int m = 0; m < nvalues; m++) vector[m] = values_global[m];
@ -527,7 +552,7 @@ void ComputeBornMatrix::compute_pairs()
void ComputeBornMatrix::compute_numdiff()
{
double energy;
int m;
int vec_indice;
// grow arrays if necessary
@ -547,6 +572,10 @@ void ComputeBornMatrix::compute_numdiff()
// loop over 6 strain directions
// compute stress finite difference in each direction
// It must be noted that, as stated in Yoshimoto's eq. 15, eq 16.
// and eq. A3, this tensor is NOT the true Cijkl tensor.
// We have the relationship
// C_ijkl=1./4.(\hat{C}_ijkl+\hat{C}_jikl+\hat{C}_ijlk+\hat{C}_jilk)
int flag, allflag;
@ -555,8 +584,8 @@ void ComputeBornMatrix::compute_numdiff()
force_clear(nall);
update_virial();
for (int jdir = 0; jdir < NDIR_VIRIAL; jdir++) {
m = revalbe[idir][jdir];
values_global[m] = compute_virial->vector[virialVtoV[jdir]];
vec_indice = revalbe[idir][jdir];
values_global[vec_indice] = compute_virial->vector[virialVtoV[jdir]];
}
restore_atoms(nall, idir);
@ -564,9 +593,11 @@ void ComputeBornMatrix::compute_numdiff()
force_clear(nall);
update_virial();
for (int jdir = 0; jdir < NDIR_VIRIAL; jdir++) {
m = revalbe[idir][jdir];
values_global[m] -= compute_virial->vector[virialVtoV[jdir]];
vec_indice = revalbe[idir][jdir];
values_global[vec_indice] -= compute_virial->vector[virialVtoV[jdir]];
}
// End of the strain
restore_atoms(nall, idir);
}
@ -588,6 +619,7 @@ void ComputeBornMatrix::compute_numdiff()
for (int i = 0; i < nall; i++)
for (int k = 0; k < 3; k++)
f[i][k] = temp_f[i][k];
}
/* ----------------------------------------------------------------------
@ -598,14 +630,22 @@ void ComputeBornMatrix::displace_atoms(int nall, int idir, double magnitude)
{
double **x = atom->x;
// this works for 7,8,9,12,14,18, and 15,16,17
// A.T.
// this works for vector indices 7, 8, 9, 12, 14, 18 and 15, 16, 17
// corresponding i,j indices 12, 13, 14, 23, 25, 36 and 26, 34, 35
int k = dirlist[idir][1];
int l = dirlist[idir][0];
// this works for 7,8,9,12,14,18, and 10,11,13
// A.T.
// this works for vector indices 7, 8, 9, 12, 14, 18 and 10, 11, 13
// corresponding i,j indices 12, 13, 14, 23, 25, 36 and 15, 16, 24
// G.C.:
// I see no difference with a 0 step simulation between both
// methods.
// int k = dirlist[idir][0];
// int l = dirlist[idir][1];
for (int i = 0; i < nall; i++)
x[i][k] = temp_x[i][k] + numdelta * magnitude * (temp_x[i][l] - fixedpoint[l]);
x[i][k] = temp_x[i][k] + numdelta * magnitude * (temp_x[i][l] - fixedpoint[l]);
}
/* ----------------------------------------------------------------------
@ -631,7 +671,8 @@ void ComputeBornMatrix::restore_atoms(int nall, int idir)
void ComputeBornMatrix::update_virial()
{
int eflag = 0;
int vflag = VIRIAL_FDOTR; // Need to generalize this
// int vflag = VIRIAL_FDOTR; // Need to generalize this
int vflag = 1;
if (force->pair) force->pair->compute(eflag, vflag);
@ -662,14 +703,17 @@ void ComputeBornMatrix::virial_addon()
// Note: in calculation kl is all there from 0 to 6, and ij=(id,jd)
// each time there are six numbers passed for (Dijkl+Djikl)
// and the term I need should be div by 2.
// Job is to arrange the 6 numbers with ij indexing to the 21 element data structure.
// Job is to arrange the 6 numbers with ij indexing to the 21
// element data structure.
// the sigv is the virial stress at current time. It is never touched.
// Note the symmetry of (i-j), (k-n), and (ij, kn)
// so we only need to evaluate 6x6 matrix with symmetry
int kd, nd, id, jd;
int m;
double* sigv = compute_virial->vector;
double modefactor[6] = {1.0, 1.0, 1.0, 0.5, 0.5, 0.5};
for (int idir = 0; idir < NDIR_VIRIAL; idir++) {
int ijvgt = idir; // this is it.
@ -680,19 +724,18 @@ void ComputeBornMatrix::virial_addon()
id = voigt3VtoM[ijvgt][0];
jd = voigt3VtoM[ijvgt][1];
int SHEAR = 0;
if( id != jd) SHEAR = 1;
for (int knvgt=ijvgt; knvgt < NDIR_VIRIAL; knvgt++) {
kd = voigt3VtoM[knvgt][0];
nd = voigt3VtoM[knvgt][1];
addon = kronecker[id][nd]*sigv[virialMtoV[jd][kd]] +
kronecker[id][kd]*sigv[virialMtoV[jd][nd]];
if(SHEAR)
if(id != jd)
addon += kronecker[jd][nd]*sigv[virialMtoV[id][kd]] +
kronecker[jd][kd]*sigv[virialMtoV[id][nd]];
values_global[revalbe[ijvgt][knvgt]] += addon;
m = revalbe[ijvgt][knvgt];
values_global[revalbe[ijvgt][knvgt]] += 0.5*modefactor[idir]*addon;
}
}
}
@ -841,7 +884,6 @@ void ComputeBornMatrix::compute_bonds()
all atoms in interaction must be known to proc
if bond is deleted or turned off (type <= 0)
do not count or count contribution
<<<<<<< HEAD
---------------------------------------------------------------------- */
void ComputeBornMatrix::compute_angles()
{