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Cyclix wraparound bug fixes #217

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Sep 5, 2024
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Cyclix wraparound bug fixes #217

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8 changes: 8 additions & 0 deletions ChangeLog
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,14 @@
-Name
-changes


--------------
September 05, 2024
Name: Abhiraj Sharma
Changes: cyclix/cyclix_tools.c, md.c, orbitalElecDens.c, forces.c
1. Wraparound bug fixed for cyclix
2. Density extrapolation fixed for cyclix

--------------
August 16, 2024
Name: Abhiraj Sharma
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0 src/cyclix/cylix_mlff/cyclix_mlff_tools.c → src/cyclix/cyclix_mlff/cyclix_mlff_tools.c
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0 src/cyclix/cylix_mlff/cyclix_mlff_tools.h → src/cyclix/cyclix_mlff/cyclix_mlff_tools.h
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2 changes: 2 additions & 0 deletions src/cyclix/cyclix_tools.c
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Expand Up @@ -211,6 +211,8 @@ void Cart2nonCart_coord_cyclix(const SPARC_OBJ *pSPARC, double *x, double *y, do
double x1, x2, x3;
x1 = sqrt((*x) * (*x) + (*y) * (*y));
x2 = atan2(*y,*x) - pSPARC->twist * (*z);
if (*y < 0.0)
x2 += 2*M_PI;
x3 = (*z);
*x = x1; *y = x2; *z = x3;
}
Expand Down
20 changes: 1 addition & 19 deletions src/forces.c
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Expand Up @@ -112,24 +112,6 @@ void Calculate_EGS_Forces(SPARC_OBJ *pSPARC)

// Apply constraint on motion of atoms for Relaxation\MD
if(pSPARC->RelaxFlag == 1 || pSPARC->MDFlag == 1) {
if (pSPARC->CyclixFlag) {
double fx, fy;
double ty, tz;
if (pSPARC->elecgs_Count > 0) {
for(i = 0; i < pSPARC->n_atom; i++){
Cart2nonCart_coord(pSPARC, &pSPARC->atom_pos_nm[3*i], &pSPARC->atom_pos_nm[3*i+1], &pSPARC->atom_pos_nm[3*i+2]);

ty = (pSPARC->atom_pos_nm[3*i+1] - pSPARC->atom_pos[3*i+1])/pSPARC->range_y;
tz = (pSPARC->atom_pos_nm[3*i+2] - pSPARC->atom_pos[3*i+2])/pSPARC->range_z;
RotMat_cyclix(pSPARC, ty, tz);
fx = pSPARC->forces[3*i]; fy = pSPARC->forces[3*i+1];
pSPARC->forces[3*i] = pSPARC->RotM_cyclix[0] * fx + pSPARC->RotM_cyclix[1] * fy;
pSPARC->forces[3*i+1] = pSPARC->RotM_cyclix[3] * fx + pSPARC->RotM_cyclix[4] * fy;

nonCart2Cart_coord(pSPARC, &pSPARC->atom_pos_nm[3*i], &pSPARC->atom_pos_nm[3*i+1], &pSPARC->atom_pos_nm[3*i+2]);
}
}
}
for(i = 0; i < 3*pSPARC->n_atom; i++)
pSPARC->forces[i] *= pSPARC->mvAtmConstraint[i];
}
Expand Down Expand Up @@ -1419,7 +1401,7 @@ void Symmetrize_forces(SPARC_OBJ *pSPARC)
shift_fy /= n_atom;
shift_fz /= n_atom;

if (pSPARC->CyclixFlag) {
if (pSPARC->CyclixFlag && pSPARC->range_y < 2.0*M_PI) {
// Do not symmetrize forces in x-y plane for cyclix systems (TODO: But do symmetrize if all the atoms are taken into account)
shift_fx = 0.0;
shift_fy = 0.0;
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12 changes: 11 additions & 1 deletion src/include/md.h
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Expand Up @@ -73,10 +73,20 @@ void Calc_vel1_G(SPARC_OBJ *pSPARC);
void Calc_vel2_G(SPARC_OBJ *pSPARC);

/*
* @ brief: function to wrap around atom positions that lie outside main domain in case of PBC and check if the atoms are too close to the boundary in case of bounded domain
* @ brief: function to check if the atoms are too close to the boundary in case of bounded domain or to each other in general
*/
void Check_atomlocation(SPARC_OBJ *pSPARC);

/*
* @ brief: function to wraparound atom positions for PBC
*/
void wraparound_dynamics(SPARC_OBJ *pSPARC, double *coord, int opt);

/*
* @ brief: function to wraparound velocities in MD and displacement vectors in relaxation for PBC
*/
void wraparound_velocity(SPARC_OBJ *pSPARC, double shift, int dir, int loc);

/*
@ brief: function to write all relevant DFT quantities generated during MD simulation
*/
Expand Down
2 changes: 1 addition & 1 deletion src/initialization.c
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Expand Up @@ -3470,7 +3470,7 @@ void write_output_init(SPARC_OBJ *pSPARC) {
}

fprintf(output_fp,"***************************************************************************\n");
fprintf(output_fp,"* SPARC (version August 16, 2024) *\n");
fprintf(output_fp,"* SPARC (version September 05, 2024) *\n");
fprintf(output_fp,"* Copyright (c) 2020 Material Physics & Mechanics Group, Georgia Tech *\n");
fprintf(output_fp,"* Distributed under GNU General Public License 3 (GPL) *\n");
fprintf(output_fp,"* Start time: %s *\n",c_time_str);
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4 changes: 2 additions & 2 deletions src/makefile
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Expand Up @@ -33,7 +33,7 @@ ENABLE_SIMD_COMPLEX = 1
# BLASROOT = /usr/lib64
# LDFLAGS += -L$(BLASROOT)

CPPFLAGS = -Iinclude/ -Ixc/exx/include -Ixc/vdW/d3/include -Ixc/vdW/vdWDF/include -Ixc/mgga/include -IhighT/include -Icyclix/include -Icyclix/cylix_mlff -IhighT/mlff_highT -Imlff/
CPPFLAGS = -Iinclude/ -Ixc/exx/include -Ixc/vdW/d3/include -Ixc/vdW/vdWDF/include -Ixc/mgga/include -IhighT/include -Icyclix/include -Icyclix/cyclix_mlff -IhighT/mlff_highT -Imlff/
LDLIBS = -lrt

ifeq ($(USE_MKL), 1)
Expand Down Expand Up @@ -102,7 +102,7 @@ OBJSC = main.o initialization.o readfiles.o atomdata.o parallelization.o relax.o
cyclix/cyclix_stress.o \
mlff/covariance_matrix.o mlff/regression.o mlff/spherical_harmonics.o mlff/soap_descriptor.o mlff/sparc_mlff_interface.o \
mlff/bessel_NR.o mlff/nrutils.o mlff/sparsification.o mlff/tools_mlff.o mlff/mlff_read_write.o \
mlff/descriptor.o mlff/ddbp_tools.o highT/mlff_highT/internal_energy_model.o cyclix/cylix_mlff/cyclix_mlff_tools.o \
mlff/descriptor.o mlff/ddbp_tools.o highT/mlff_highT/internal_energy_model.o cyclix/cyclix_mlff/cyclix_mlff_tools.o \
mlff/hnl_soap.o

LIBBASE = ../lib/sparc
Expand Down
79 changes: 64 additions & 15 deletions src/md.c
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Expand Up @@ -1768,7 +1768,7 @@ void Cart2nonCart(double *gradT, double *carCoord, double *nonCarCoord) {
}

/*
@ brief: function to wrap around atom positions that lie outside main domain in case of PBC and check if the atoms are too close to the boundary in case of bounded domain
* @ brief: function to check if the atoms are too close to the boundary in case of bounded domain or to each other in general
*/
void Check_atomlocation(SPARC_OBJ *pSPARC) {
int rank, ityp, i, atm, atm2, count, dir = 0, maxdir = 3, BC;
Expand Down Expand Up @@ -1813,10 +1813,22 @@ void Check_atomlocation(SPARC_OBJ *pSPARC) {
}
free(rc);

wraparound_dynamics(pSPARC, pSPARC->atom_pos, 1);
}

/*
* @ brief: function to wraparound atom positions for PBC
*/
void wraparound_dynamics(SPARC_OBJ *pSPARC, double *coord, int opt) {

int rank, atm, dir = 0, maxdir = 3, BC;
double length, coord_temp;// Change tol according to the situation
MPI_Comm_rank(MPI_COMM_WORLD,&rank);

// Convert Cart to nonCart coordinates for non orthogonal cell
if(pSPARC->cell_typ != 0){
for(atm = 0; atm < pSPARC->n_atom; atm++)
Cart2nonCart_coord(pSPARC, &pSPARC->atom_pos[3*atm], &pSPARC->atom_pos[3*atm+1], &pSPARC->atom_pos[3*atm+2]);
Cart2nonCart_coord(pSPARC, coord+3*atm, coord+3*atm+1, coord+3*atm+2);
}

while(dir < maxdir){
Expand All @@ -1834,27 +1846,64 @@ void Check_atomlocation(SPARC_OBJ *pSPARC) {
}
if(BC == 1){
if (!((pSPARC->CyclixFlag) && (dir == 0))) { // if it is in cyclix coordinate and in x (radial) direction, we will not check it
for(atm = 0; atm < pSPARC->n_atom; atm++){
if(pSPARC->atom_pos[atm * 3 + dir] >= length || pSPARC->atom_pos[atm * 3 + dir] < 0){
if(!rank)
printf("ERROR: Atom number %d has crossed the boundary in %d direction",atm, dir);
exit(EXIT_FAILURE);
for(atm = 0; atm < pSPARC->n_atom; atm++){
if(coord[atm * 3 + dir] >= length || coord[atm * 3 + dir] < 0){
if(!rank)
printf("ERROR: Atom number %d has crossed the boundary in %d direction",atm, dir);
exit(EXIT_FAILURE);
}
}
}
} else if(BC == 0){
for(atm = 0; atm < pSPARC->n_atom; atm++){
coord_temp = *(coord+3*atm+dir);
if (coord_temp < 0.0 || coord_temp >= length)
{
coord_temp = fmod(coord_temp,length);
double new_coord = coord_temp + (coord_temp<0.0)*length;
double shift = new_coord - *(coord+3*atm+dir);
*(coord+3*atm+dir) = new_coord;
if (pSPARC->CyclixFlag && opt == 1){
wraparound_velocity(pSPARC, shift, dir, 3*atm);
}
}
}
}else if(BC == 0){
// TODO: Assumed that atom moves less than one cell length, generalize in future
for(atm = 0; atm < pSPARC->n_atom; atm++){
if(pSPARC->atom_pos[atm * 3 + dir] >= length)
pSPARC->atom_pos[atm * 3 + dir] -= length;
else if(pSPARC->atom_pos[atm * 3 + dir] < 0)
pSPARC->atom_pos[atm * 3 + dir] += length;
}
}
dir ++;
}
}

/*
* @ brief: function to wraparound velocities in MD and displacement vectors in relaxation for PBC
*/
void wraparound_velocity(SPARC_OBJ *pSPARC, double shift, int dir, int loc) {

if (dir == 1){
if (pSPARC->MDFlag == 1){
double vx = pSPARC->ion_vel[loc]; double vy = pSPARC->ion_vel[loc+1];
pSPARC->ion_vel[loc] = cos(shift) * vx -sin(shift) * vy;
pSPARC->ion_vel[loc+1] = sin(shift) * vx + cos(shift) * vy;
}
else if (pSPARC->RelaxFlag == 1){
double vx = pSPARC->d[loc]; double vy = pSPARC->d[loc+1];
pSPARC->d[loc] = cos(shift) * vx -sin(shift) * vy;
pSPARC->d[loc+1] = sin(shift) * vx + cos(shift) * vy;
}
} else if (dir == 2){
if (pSPARC->MDFlag == 1){
double vx = pSPARC->ion_vel[loc]; double vy = pSPARC->ion_vel[loc+1];
pSPARC->ion_vel[loc] = cos(pSPARC->twist*shift) * vx -sin(pSPARC->twist*shift) * vy;
pSPARC->ion_vel[loc+1] = sin(pSPARC->twist*shift) * vx + cos(pSPARC->twist*shift) * vy;
}
else if (pSPARC->RelaxFlag == 1){
double vx = pSPARC->d[loc]; double vy = pSPARC->d[loc+1];
pSPARC->d[loc] = cos(pSPARC->twist*shift) * vx -sin(pSPARC->twist*shift) * vy;
pSPARC->d[loc+1] = sin(pSPARC->twist*shift) * vx + cos(pSPARC->twist*shift) * vy;
}
}

}

/*
@ brief: function to write all relevant DFT quantities generated during MD simulation
*/
Expand Down
107 changes: 77 additions & 30 deletions src/orbitalElecDensInit.c
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Expand Up @@ -28,6 +28,8 @@
#include "electronDensity.h"
#include "parallelization.h"
#include "readfiles.h"
#include "initialization.h"
#include "md.h"
#define max(x,y) ((x)>(y)?(x):(y))


Expand Down Expand Up @@ -205,47 +207,93 @@ void Init_electronDensity(SPARC_OBJ *pSPARC) {
*/
// TODO: Check if the FtF matrix is singular and if it is then decide on how to do extrapolation or not to do at all
void elecDensExtrapolation(SPARC_OBJ *pSPARC) {
// processors that are not in the dmcomm_phi will remain idle
// processors that are not in the dmcomm_phi will remain idle
if (pSPARC->dmcomm_phi == MPI_COMM_NULL) {
return;
}
int nd, ii, matrank, count = 0, atm;
double alpha, beta;
double alpha, beta, *coord_temp1, *coord_temp2;
for (nd = 0; nd < pSPARC->Nd_d; nd++){
pSPARC->delectronDens_2dt[nd] = pSPARC->delectronDens_1dt[nd];
pSPARC->delectronDens_1dt[nd] = pSPARC->delectronDens_0dt[nd];
pSPARC->delectronDens_0dt[nd] = pSPARC->electronDens[nd] - pSPARC->electronDens_at[nd];
double *electronDens = pSPARC->electronDens;
pSPARC->delectronDens_0dt[nd] = electronDens[nd] - pSPARC->electronDens_at[nd];
}
if(pSPARC->MDFlag == 1){
for(atm = 0; atm < pSPARC->n_atom; atm++){
if(pSPARC->MDCount == 1){
pSPARC->atom_pos_nm[count * 3] = pSPARC->atom_pos[count * 3];
pSPARC->atom_pos_nm[count * 3 + 1] = pSPARC->atom_pos[count * 3 + 1];
pSPARC->atom_pos_nm[count * 3 + 2] = pSPARC->atom_pos[count * 3 + 2];
count ++;
} else{
pSPARC->atom_pos_nm[count * 3] += pSPARC->MD_dt * pSPARC->ion_vel[count * 3];
pSPARC->atom_pos_nm[count * 3 + 1] += pSPARC->MD_dt * pSPARC->ion_vel[count * 3 + 1];
pSPARC->atom_pos_nm[count * 3 + 2] += pSPARC->MD_dt * pSPARC->ion_vel[count * 3 + 2];
count ++;
}
}
if(pSPARC->MDCount == 1) {
for(atm = 0; atm < pSPARC->n_atom; atm++){
pSPARC->atom_pos_nm[count * 3] = pSPARC->atom_pos[count * 3];
pSPARC->atom_pos_nm[count * 3 + 1] = pSPARC->atom_pos[count * 3 + 1];
pSPARC->atom_pos_nm[count * 3 + 2] = pSPARC->atom_pos[count * 3 + 2];
count ++;
}
} else{
coord_temp1 = (double *) malloc(3*pSPARC->n_atom*sizeof(double));
coord_temp2 = (double *) malloc(3*pSPARC->n_atom*sizeof(double));

for(atm = 0; atm < 3*pSPARC->n_atom; atm++){
coord_temp1[atm] = pSPARC->atom_pos_nm[atm];
coord_temp2[atm] = pSPARC->atom_pos[atm];
}
wraparound_dynamics(pSPARC, coord_temp1, 0);
if(pSPARC->cell_typ != 0){
for(atm = 0; atm < pSPARC->n_atom; atm++){
Cart2nonCart_coord(pSPARC, coord_temp2+3*atm, coord_temp2+3*atm+1, coord_temp2+3*atm+2);
Cart2nonCart_coord(pSPARC, pSPARC->atom_pos_nm+3*atm, pSPARC->atom_pos_nm+3*atm+1, pSPARC->atom_pos_nm+3*atm+2);
}
}
for(atm = 0; atm < 3*pSPARC->n_atom; atm++){
pSPARC->atom_pos_nm[atm] += coord_temp2[atm] - coord_temp1[atm];
}



if(pSPARC->cell_typ != 0){
for(atm = 0; atm < pSPARC->n_atom; atm++){
nonCart2Cart_coord(pSPARC, pSPARC->atom_pos_nm+3*atm, pSPARC->atom_pos_nm+3*atm+1, pSPARC->atom_pos_nm+3*atm+2);
}
}

free(coord_temp1);
free(coord_temp2);
}
} else if(pSPARC->RelaxFlag == 1){
for(atm = 0; atm < pSPARC->n_atom; atm++){
if((pSPARC->elecgs_Count - pSPARC->StressCount) == 1){
pSPARC->atom_pos_nm[count * 3] = pSPARC->atom_pos[count * 3];
pSPARC->atom_pos_nm[count * 3 + 1] = pSPARC->atom_pos[count * 3 + 1];
pSPARC->atom_pos_nm[count * 3 + 2] = pSPARC->atom_pos[count * 3 + 2];
if((pSPARC->elecgs_Count - pSPARC->StressCount) == 1) {
for(atm = 0; atm < pSPARC->n_atom; atm++){
pSPARC->atom_pos_nm[count * 3] = pSPARC->atom_pos[count * 3];
pSPARC->atom_pos_nm[count * 3 + 1] = pSPARC->atom_pos[count * 3 + 1];
pSPARC->atom_pos_nm[count * 3 + 2] = pSPARC->atom_pos[count * 3 + 2];
count ++;
} else{
pSPARC->atom_pos_nm[count * 3] += pSPARC->Relax_fac * pSPARC->d[count * 3] * pSPARC->mvAtmConstraint[count * 3];
pSPARC->atom_pos_nm[count * 3 + 1] += pSPARC->Relax_fac * pSPARC->d[count * 3 + 1] * pSPARC->mvAtmConstraint[count * 3 + 1];
pSPARC->atom_pos_nm[count * 3 + 2] += pSPARC->Relax_fac * pSPARC->d[count * 3 + 2] * pSPARC->mvAtmConstraint[count * 3 + 2];
count ++;
}
}
}
} else{
coord_temp1 = (double *) malloc(3*pSPARC->n_atom*sizeof(double));
coord_temp2 = (double *) malloc(3*pSPARC->n_atom*sizeof(double));

for(atm = 0; atm < 3*pSPARC->n_atom; atm++){
coord_temp1[atm] = pSPARC->atom_pos_nm[atm];
coord_temp2[atm] = pSPARC->atom_pos[atm];
}
wraparound_dynamics(pSPARC, coord_temp1, 0);
if(pSPARC->cell_typ != 0){
for(atm = 0; atm < pSPARC->n_atom; atm++){
Cart2nonCart_coord(pSPARC, coord_temp2+3*atm, coord_temp2+3*atm+1, coord_temp2+3*atm+2);
Cart2nonCart_coord(pSPARC, pSPARC->atom_pos_nm+3*atm, pSPARC->atom_pos_nm+3*atm+1, pSPARC->atom_pos_nm+3*atm+2);
}
}
for(atm = 0; atm < 3*pSPARC->n_atom; atm++){
pSPARC->atom_pos_nm[atm] += coord_temp2[atm] - coord_temp1[atm];
}

if(pSPARC->cell_typ != 0){
for(atm = 0; atm < pSPARC->n_atom; atm++)
nonCart2Cart_coord(pSPARC, pSPARC->atom_pos_nm+3*atm, pSPARC->atom_pos_nm+3*atm+1, pSPARC->atom_pos_nm+3*atm+2);
}

free(coord_temp1);
free(coord_temp2);
}
}
if((pSPARC->elecgs_Count - pSPARC->StressCount) >= 3){
if((pSPARC->elecgs_Count - pSPARC->StressCount) >= 3){
double *FtF, *Ftf, *s, temp1, temp2, temp3; // 2x2 matrix and 2x1 vectors in (FtF)*(svec) = Ftf
FtF = (double *)calloc( 4 , sizeof(double) );
Ftf = (double *)calloc( 2 , sizeof(double) );
Expand Down Expand Up @@ -279,7 +327,6 @@ void elecDensExtrapolation(SPARC_OBJ *pSPARC) {
}
}


/**
* @brief initialize Kohn-Sham orbitals.
*/
Expand Down
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