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1) Added born_matrix method to bond_harmonic, angle_cosine_squared and dihedral_nharmonic

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2) Changed compute_born_matrix so it can takes arguments pair bond angle dihedral to output only selected elements. Also moved flags to creator method and added error/warning messages
This commit is contained in:
Germain Clavier
2022-02-06 20:00:55 +01:00
parent 5142934a26
commit a110b1d475
7 changed files with 215 additions and 58 deletions
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164
src/EXTRA-COMPUTE/compute_born_matrix.cpp
View File

@ -43,13 +43,26 @@ using namespace LAMMPS_NS;
#define BIG 1000000000
static int const albe[21][2] = {
// This table is used to pick the 3d rij vector indices used to
// compute the 6 indices long Voigt stress vector
static int const sigma_albe[6][2] = {
{0, 0}, // s11
{1, 1}, // s22
{2, 2}, // s33
{1, 2}, // s44
{0, 2}, // s55
{0, 1}, // s66
};
// This table is used to pick the correct indices from the Voigt
// stress vector to compute the Cij matrix (21 terms, see doc) contribution
static int const C_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
@ -67,6 +80,8 @@ static int const albe[21][2] = {
{4, 5} // C56
};
// This table is used to pick the 3d rij vector indices used to
// compute the 21 indices long Cij matrix
static int const albemunu[21][4] = {
{0, 0, 0, 0}, // C11
{1, 1, 1, 1}, // C22
@ -103,6 +118,75 @@ ComputeBornMatrix::ComputeBornMatrix(LAMMPS *lmp, int narg, char **arg) : Comput
// Error check
if (narg < 3) error->all(FLERR,"Illegal compute pressure command");
pairflag = 0;
bondflag = 0;
angleflag = 0;
dihedflag = 0;
impflag = 0;
kspaceflag = 0;
if (narg == 3) {
pairflag = 1;
bondflag = 1;
angleflag = 1;
dihedflag = 1;
impflag = 1;
kspaceflag = 1;
} else {
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) impflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else error->all(FLERR,"Illegal compute pressure command");
++iarg;
}
}
// Error check
if (pairflag) {
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");
}
}
}
if (bondflag) {
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");
}
}
}
if (angleflag) {
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");
}
}
}
if (dihedflag) {
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");
}
}
}
if (impflag) {
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");
}
}
}
if (kspaceflag) {
error->warning(FLERR, "KSPACE contribution not supported by compute born/matrix");
}
// Initialize some variables
values_local = values_global = vector = nullptr;
@ -138,42 +222,16 @@ void ComputeBornMatrix::init()
// Timestep Value
dt = update->dt;
pairflag = 0;
bondflag = 0;
angleflag = 0;
dihedflag = 0;
impflag = 0;
kspaceflag = 0;
// IF everything works fine,
// this is to be removed
//
// if (force->pair) pairflag = 1;
// if (force->bond) bondflag = 1;
// if (force->angle) angleflag = 1;
// if (force->dihedral) dihedflag = 1;
// if (force->improper) impflag = 1;
// if (force->kspace) kspaceflag = 1;
if (force->pair) pairflag = 1;
if (force->bond) bondflag = 1;
if (force->angle) angleflag = 1;
if (force->dihedral) dihedflag = 1;
if (force->improper) impflag = 1;
if (force->kspace) kspaceflag = 1;
// Error check
if (comm->me == 0) {
if (pairflag && (force->pair->born_matrix_enable == 0)) {
error->all(FLERR, "Pair style does not support compute born/matrix");
}
if (bondflag && (force->bond->born_matrix_enable == 0)) {
error->warning(FLERR, "Bond style does not support compute born/matrix");
}
if (angleflag && (force->angle->born_matrix_enable == 0)) {
error->warning(FLERR, "Angle style does not support compute born/matrix");
}
if (dihedflag && (force->dihedral->born_matrix_enable == 0)) {
error->warning(FLERR, "Dihedral style does not support compute born/matrix");
}
if (impflag && (force->improper->born_matrix_enable == 0)) {
error->warning(FLERR, "Improper style does not support compute born/matrix");
}
if (kspaceflag) {
error->warning(FLERR, "KSPACE contribution not supported by compute born/matrix");
}
}
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
@ -204,7 +262,6 @@ void ComputeBornMatrix::compute_vector()
// Compute Born contribution
if (pairflag) compute_pairs();
// For now these functions are commented
if (bondflag) compute_bonds();
if (angleflag) compute_angles();
if (dihedflag) compute_dihedrals();
@ -331,11 +388,9 @@ void ComputeBornMatrix::compute_pairs()
all atoms in interaction must be known to proc
if bond is deleted or turned off (type <= 0)
do not count or count contribution
COMMENTED FOR NOW
---------------------------------------------------------------------- */
void ComputeBornMatrix::compute_bonds()
{
/* ----------------------------------------------------------------------
int i,m,n,nb,atom1,atom2,imol,iatom,btype,ivar;
tagint tagprev;
double dx,dy,dz,rsq;
@ -426,7 +481,6 @@ void ComputeBornMatrix::compute_bonds()
}
m += 21;
}
------------------------------------------------------------------------- */
}
/* ----------------------------------------------------------------------
@ -436,11 +490,9 @@ 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
COMMENTED FOR NOW
---------------------------------------------------------------------- */
void ComputeBornMatrix::compute_angles()
{
/* ----------------------------------------------------------------------
int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype,ivar;
tagint tagprev;
double delx1,dely1,delz1,delx2,dely2,delz2;
@ -568,8 +620,8 @@ void ComputeBornMatrix::compute_angles()
c = 0;
d = 0;
for (i = 0; i<6; i++) {
a = albe[i][0];
b = albe[i][1];
a = sigma_albe[i][0];
b = sigma_albe[i][1];
dcos[i] = cost*(del1[a]*del2[b]+del1[b]*del2[a]*r1r2inv -
del1[a]*del1[b]*rsq1inv - del2[a]*del2[b]*rsq2inv);
}
@ -578,8 +630,8 @@ void ComputeBornMatrix::compute_angles()
b = albemunu[i][1];
c = albemunu[i][2];
d = albemunu[i][3];
e = albe[i][0];
f = albe[i][1];
e = C_albe[i][0];
f = C_albe[i][1];
d2lncos[i] = 2*(del1[a]*del1[b]*del1[c]*del1[d]*rsq1inv*rsq1inv +
del2[a]*del2[b]*del2[c]*del2[d]*rsq2inv*rsq2inv) -
(del1[a]*del2[b]+del1[b]*del2[a]) *
@ -592,7 +644,6 @@ void ComputeBornMatrix::compute_angles()
}
m+=21;
}
------------------------------------------------------------------------- */
}
/* ----------------------------------------------------------------------
@ -601,12 +652,10 @@ void ComputeBornMatrix::compute_angles()
all atoms in interaction must be in group
all atoms in interaction must be known to proc
if flag is set, compute requested info about dihedral
COMMENTED FOR NOW
------------------------------------------------------------------------- */
void ComputeBornMatrix::compute_dihedrals()
{
/* ----------------------------------------------------------------------
int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom,dtype,ivar;
tagint tagprev;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
@ -781,8 +830,8 @@ void ComputeBornMatrix::compute_dihedrals()
e = 0;
f = 0;
for (i = 0; i<6; i++) {
a = albe[i][0];
b = albe[i][1];
a = sigma_albe[i][0];
b = sigma_albe[i][1];
dmm[i] = 2*(b2sq*b1[a]*b1[b]+b1sq*b2[a]*b2[b] - b1b2*(b1[a]*b2[b]+b1[b]*b2[a]));
dnn[i] = 2*(b3sq*b2[a]*b2[b]+b2sq*b3[a]*b3[b] - b2b3*(b2[a]*b3[b]+b2[b]*b3[a]));
dmn[i] = b1b2*(b2[a]*b3[b]+b2[b]*b3[a]) + b2b3*(b1[a]*b2[b]+b1[b]*b2[a])
@ -794,8 +843,8 @@ void ComputeBornMatrix::compute_dihedrals()
b = albemunu[i][1];
c = albemunu[i][2];
d = albemunu[i][3];
e = albe[i][0];
f = albe[i][1];
e = C_albe[i][0];
f = C_albe[i][1];
d2mm[i] = 4*(b1[a]*b1[b]*b2[c]*b2[d] + b1[c]*b1[d]*b2[a]*b2[b])
- 8*(b1[a]*b2[b]+b1[b]*b2[a])*(b1[c]*b2[d]+b1[d]*b2[c]);
d2nn[i] = 4*(b2[a]*b2[b]*b3[c]*b3[d] + b2[c]*b2[d]*b3[a]*b3[b])
@ -810,12 +859,11 @@ void ComputeBornMatrix::compute_dihedrals()
+ ra2inv*ra2inv*dmm[e]*dmm[f]
- ra2inv*d2mm[i]
+ rb2inv*rb2inv*dnn[e]*dnn[f]
- rb2inv*d2nn[i] );
- rb2inv*d2nn[i]);
values_local[m+i] += dudih*d2cos[i] + du2dih*dcos[e]*dcos[f];
}
}
}
m+=21;
}
------------------------------------------------------------------------- */
}

61
src/EXTRA-MOLECULE/dihedral_nharmonic.cpp
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@ -39,6 +39,7 @@ DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp)
{
writedata = 1;
a = nullptr;
born_matrix_enable = 1;
}
/* ---------------------------------------------------------------------- */
@ -336,3 +337,63 @@ void DihedralNHarmonic::write_data(FILE *fp)
}
}
/* ----------------------------------------------------------------------*/
void DihedralNHarmonic::born_matrix(int nd, int i1, int i2, int i3, int i4,
double &dudih, double &du2dih) {
int i,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double c,s,kf;
int **dihedrallist = neighbor->dihedrallist;
double **x = atom->x;
type = dihedrallist[nd][4];
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
ra2inv = rb2inv = 0.0;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
dudih = 0.0;
du2dih = 0.0;
for (i = 1; i < nterms[type]; i++) {
dudih += this->a[type][i]*i*pow(c,i-1);
}
for (i = 2; i < nterms[type]; i++) {
du2dih += this->a[type][i]*i*(i-1)*pow(c, i-2);
}
}

1
src/EXTRA-MOLECULE/dihedral_nharmonic.h
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@ -33,6 +33,7 @@ class DihedralNHarmonic : public Dihedral {
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void born_matrix(int /*dtype*/, int, int, int, int, double&, double&);
protected:
int *nterms;

30
src/MOLECULE/angle_cosine_squared.cpp
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@ -40,6 +40,7 @@ AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp)
{
k = nullptr;
theta0 = nullptr;
born_matrix_enable = 1;
}
/* ---------------------------------------------------------------------- */
@ -263,3 +264,32 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3)
double tk = k[type] * dcostheta;
return tk*dcostheta;
}
/* ---------------------------------------------------------------------- */
void AngleCosineSquared::born_matrix(int type, int i1, int i2, int i3, double& du, double& du2)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double dcostheta = c - cos(theta0[type]);
double tk = k[type] * dcostheta;
du2 = 2*k[type];
du = du2*dcostheta;
}

1
src/MOLECULE/angle_cosine_squared.h
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@ -35,6 +35,7 @@ class AngleCosineSquared : public Angle {
void read_restart(FILE *);
void write_data(FILE *);
virtual double single(int, int, int, int);
void born_matrix(int type, int i1, int i2, int i3, double& du, double& du2);
protected:
double *k, *theta0;

15
src/MOLECULE/bond_harmonic.cpp
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@ -31,6 +31,7 @@ using namespace LAMMPS_NS;
BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
{
reinitflag = 1;
born_matrix_enable = 1;
}
/* ---------------------------------------------------------------------- */
@ -201,6 +202,20 @@ double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/,
return rk*dr;
}
/* ---------------------------------------------------------------------- */
void BondHarmonic::born_matrix(int type, double rsq, int /*i*/, int /*j*/,
double &du, double& du2)
{
double r = sqrt(rsq);
double dr = r - r0[type];
du2 = 0.0;
du = 0.0;
du2 = 2*k[type];
if (r > 0.0) du = du2*dr;
}
/* ----------------------------------------------------------------------
Return ptr to internal members upon request.
------------------------------------------------------------------------ */

1
src/MOLECULE/bond_harmonic.h
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@ -35,6 +35,7 @@ class BondHarmonic : public Bond {
virtual void read_restart(FILE *);
void write_data(FILE *);
double single(int, double, int, int, double &);
void born_matrix(int, double, int, int, double &, double &);
virtual void *extract(const char *, int &);
protected: