tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Got all the pieces in, now just need to get the right answer

Browse Source
This commit is contained in:
Aidan Thompson
2022-01-30 15:52:16 -07:00
parent 0f85809acf
commit cc9c578006
3 changed files with 54 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/cij_nvt/in.ljfcc_num
View File

@ -6,7 +6,7 @@
variable nsteps index 50 # length of run
variable nthermo index 10 # thermo output interval
variable nlat index 3 # size of box
variable delta index 1.0e-6 # strain size
variable delta index 1.0e-4 # strain size
variable temp index 0.3 # temperature
units lj

81
src/EXTRA-COMPUTE/compute_born_matrix.cpp
View File

@ -51,9 +51,9 @@ static int constexpr albe[21][2] = {
{0, 0}, // C11
{1, 1}, // C22
{2, 2}, // C33
{1, 2}, // C44
{0, 2}, // C55
{0, 1}, // C66
{3, 3}, // C44
{4, 4}, // C55
{5, 5}, // C66
{0, 1}, // C12
{0, 2}, // C13
{0, 3}, // C14
@ -97,7 +97,9 @@ static int constexpr albemunu[21][4] = {
/* ---------------------------------------------------------------------- */
ComputeBornMatrix::ComputeBornMatrix(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
ComputeBornMatrix::ComputeBornMatrix(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), id_virial(nullptr), temp_x(nullptr),
temp_f(nullptr)
{
if (narg < 3) error->all(FLERR,"Illegal compute born/matrix command");
@ -112,6 +114,7 @@ ComputeBornMatrix::ComputeBornMatrix(LAMMPS *lmp, int narg, char **arg) : Comput
if (iarg+3 > narg) error->all(FLERR,"Illegal compute born/matrix command");
numflag = 1;
numdelta = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (numdelta <= 0.0) error->all(FLERR, "Illegal compute born/matrix command");
id_virial = utils::strdup(arg[iarg+2]);
int icompute = modify->find_compute(id_virial);
if (icompute < 0) error->all(FLERR,"Could not find compute born/matrix pressure ID");
@ -184,7 +187,6 @@ ComputeBornMatrix::~ComputeBornMatrix()
} else {
memory->destroy(temp_x);
memory->destroy(temp_f);
modify->delete_compute(id_virial);
delete[] id_virial;
}
@ -258,6 +260,13 @@ void ComputeBornMatrix::init()
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");
}
// voigt3VtoM notation in normal physics sense,
// 3x3 matrix and vector indexing
// i-j: (1-1), (2-2), (3-3), (2-3), (1-3), (1-2)
@ -291,6 +300,14 @@ void ComputeBornMatrix::init()
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
int indcounter = 0;
for(int row = 0; row < NDIR_VIRIAL; row++)
for(int col = row; col< NDIR_VIRIAL; col++) {
voigt6MtoV[row][col] = voigt6MtoV[col][row] = indcounter;
indcounter++;
}
// set up 3x3 kronecker deltas
for(int row = 0; row < NXYZ_VIRIAL; row++)
@ -314,7 +331,7 @@ void ComputeBornMatrix::init_list(int /* id */, NeighList *ptr)
void ComputeBornMatrix::compute_vector()
{
invoked_array = update->ntimestep;
invoked_vector = update->ntimestep;
if (!numflag) {
@ -457,13 +474,13 @@ void ComputeBornMatrix::compute_numdiff()
// grow arrays if necessary
if (atom->nlocal + atom->nghost > maxatom) reallocate();
int nall = atom->nlocal + atom->nghost;
if (nall > maxatom) reallocate();
// store copy of current forces for owned and ghost atoms
double **x = atom->x;
double **f = atom->f;
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++)
for (int k = 0; k < 3; k++) {
@ -496,7 +513,15 @@ void ComputeBornMatrix::compute_numdiff()
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;
// recompute virial so all virial and energy contributions are as before
// also needed for virial stress addon contributions to Born matrix
// this will possibly break compute stress/atom, need to test
update_virial();
@ -507,11 +532,6 @@ void ComputeBornMatrix::compute_numdiff()
for (int k = 0; k < 3; k++)
f[i][k] = temp_f[i][k];
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;
virial_addon();
@ -549,9 +569,9 @@ void ComputeBornMatrix::restore_atoms(int nall, int idir)
void ComputeBornMatrix::update_virial()
{
int eflag = 0;
int vflag = 1;
int vflag = VIRIAL_FDOTR; // Need to generalize this
if (pairflag) force->pair->compute(eflag, vflag);
if (force->pair) force->pair->compute(eflag, vflag);
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag, vflag);
@ -560,16 +580,16 @@ void ComputeBornMatrix::update_virial()
if (force->improper) force->improper->compute(eflag, vflag);
}
if (kspaceflag) force->kspace->compute(eflag, vflag);
if (force->kspace) force->kspace->compute(eflag, vflag);
compute_virial->compute_vector();
}
/* ----------------------------------------------------------------------
calculate extra virial terms
following code of Dr. Yubao Zhen
Comp. Phys. Comm. 183 (2012) 261-265
calculate virial stress addon terms to the Born matrix
this is based on original code of Dr. Yubao Zhen
described here: Comp. Phys. Comm. 183 (2012) 261-265
------------------------------------------------------------------------- */
void ComputeBornMatrix::virial_addon()
@ -591,23 +611,26 @@ void ComputeBornMatrix::virial_addon()
double* sigv = compute_virial->vector;
for (int idir = 0; idir < NDIR_VIRIAL; idir++) {
int ijvgt = idir; // this is it.
int ijvgt = idir; // this is it.
double addon;
id = voigt3VtoM[idir][0]; // extract the two indicies composing the voigt reprensentation
// extract the two indicies composing the voigt reprensentation
id = voigt3VtoM[idir][0];
jd = voigt3VtoM[idir][1];
int SHEAR = 0;
if( id != jd) SHEAR = 1;
// note BornVec must be cleared before.
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)
addon = addon + kronecker[jd][nd]*sigv[virialMtoV[id][kd]] + kronecker[jd][kd]*sigv[virialMtoV[id][nd]];
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)
addon += kronecker[jd][nd]*sigv[virialMtoV[id][kd]] +
kronecker[jd][kd]*sigv[virialMtoV[id][nd]];
values_global[voigt6MtoV[ijvgt][knvgt]] += addon;
}
}
}

1
src/EXTRA-COMPUTE/compute_born_matrix.h
View File

@ -75,6 +75,7 @@ class ComputeBornMatrix : public Compute {
int voigt3VtoM[NDIR_VIRIAL][2];
int voigt3MtoV[NXYZ_VIRIAL][NXYZ_VIRIAL];
int virialMtoV[NXYZ_VIRIAL][NXYZ_VIRIAL];
int voigt6MtoV[NDIR_VIRIAL][NDIR_VIRIAL];
int kronecker[NXYZ_VIRIAL][NXYZ_VIRIAL];
double **temp_x; // original coords
double **temp_f; // original forces