/*!
@brief Initialize iteration over an object.
@ingroup iterate
@param object Object to be iterated over.
@param iter Iterator reference.
@see v_iterate()
*/
void
v_iter(void *object, viter *iter)
{
V_ZERO(iter, 1);
iter->object = object;
iter->count = -1;
}
/* COMPUTATION OF FORCES BETWEEN NON-CONNECTED BEADS AND BEADS-SUBSTRATE_ATOMS(with neighbor-list) */
void ComputeForcesPT () {
VecR dr, dv; // distance and velocity difference between i- and j- beads (VECTORS)
real scal, fDispRand, fDisp, fRand, theta, uVal, omega_r, omega_d; // dissipative and random forces variables
real fcVal, rr, rri, rri3;
int j1, j2, n;
int N0, j, N_j1, N_j2, j_min, j_max, top; // slabs profile variable
real dTop, dBot, xx, yy, zz, zi; // distances for pressure tensor variables (dTop - upper particle, dBot - bottom particle)
real secTermX, secTermY, secTermZ, secTermXY; // pressure tensor calculating
VecR invWid, rs;
VecI cc;
int c, hSize;
real uValPP, uValPS; // polymer-polymer and polymer-surface energies
DO_MOL V_ZERO (mol[n].ra);
uSum = 0.;
U_LJ_sub = 0.;
virSum = 0.;
uValPP = uValPS = 0.;
V_ZERO (force1);
V_ZERO (force2);
V_ZERO (forceT);
/* set all substrate Unit - polymer liquid interactions to zero */
for (n = -1; n < totSUnitNum; n++) {
enLJSUnit[n] = 0.;
}
if ((stepCount > stepEquil) && (stepCount - stepEquil) % stepConVal == 0) {
hSize = V_PROD (sizeVelGrid); // number of grid cells in the system
/* setting initial snapshots values to zero */
for (j = 0; j < NHIST_E; j++) {
for (n = 0; n < hSize; n++) snapEnGrid[j][n] = 0.;
}
}
for (n = 0; n < nebrTabLen; n++) {
j1 = nebrTab[2 * n];
j2 = nebrTab[2 * n + 1];
if ((mol[j1].inChain == -1) && (mol[j2].inChain == -1)) {
}
else {
V_SUB (dr, mol[j1].r, mol[j2].r);
V_WRAP_ALL (dr);
rr = V_LEN_SQ (dr);
if (rr < rrCut) {
/* defining slab contains j1 */
if (mol[j1].r.z < 0.)
N_j1 = halfSl - (int) (-mol[j1].r.z / hSlab) - 1;
else
N_j1 = halfSl + (int) (mol[j1].r.z / hSlab);
/* defining slab contains j2 */
if (mol[j2].r.z < 0.)
N_j2 = halfSl - (int) (-mol[j2].r.z / hSlab) - 1;
else
N_j2 = halfSl + (int) (mol[j2].r.z / hSlab);
/* x, y, z-distances between two beads (squared) */
xx = SQR(dr.x);
yy = SQR(dr.y);
zz = SQR(dr.z);
zi = 1. / sqrt (zz);
/* min and max slabs, containing interacting particles */
if (N_j1 > N_j2) {
j_max = N_j1;
j_min = N_j2;
top = 1;
/* defining distances to desired slab boundaries */
if (j_max - j_min < halfSl) {
dTop = mol[j1].r.z - hSlab * (j_max - halfSl);
dBot = hSlab * (j_min - halfSl + 1) - mol[j2].r.z;
} else {
dTop = hSlab * (j_max - halfSl + 1) - mol[j1].r.z;
dBot = mol[j2].r.z + hSlab * (halfSl - j_min);
}
} else if (N_j1 < N_j2) {
j_max = N_j2;
j_min = N_j1;
top = 2;
/* defining distances to desired slab boundaries */
if (j_max - j_min < halfSl) {
dTop = mol[j2].r.z - hSlab * (j_max - halfSl);
dBot = hSlab * (j_min - halfSl + 1) - mol[j1].r.z;
} else {
dTop = hSlab * (j_max - halfSl + 1) - mol[j2].r.z;
dBot = mol[j1].r.z + hSlab * (halfSl - j_min);
}
} else if (N_j1 == N_j2) {
j_max = N_j1;
j_min = N_j1;
top = 0;
}
/* Lennard-Jones forces */
rri = 1. / rr;
rri3 = CUBE (rri);
if ((mol[j1].inChain != -1) && (mol[j2].inChain != -1)) { // interaction of nonbonded chain particles
fcVal = 48. * rri3 * (rri3 - 0.5) * rri;
uVal = 4. * rri3 * (rri3 - 1.) - U0;
uValPP = uVal;
uValPS = 0.;
V_V_S_ADD (mol[j1].ra, fcVal, dr);
V_V_S_ADD (mol[j2].ra, -fcVal, dr);
} else if ((mol[j1].inChain == -1) && (mol[j1].inSUnit != -2) && (mol[j2].inChain != -1)) {
fcVal = 48. * epsWall * rri3 * ss3_sur * (rri3 * ss3_sur - 0.5) * rri; // interaction with the substrate
uVal = 4. * epsWall * rri3 * ss3_sur * (rri3 * ss3_sur - 1.) - U0_surf;
U_LJ_sub += uVal;
uValPP = 0.;
uValPS = uVal;
if ((stepCount > stepEquil) && (stepCount - stepEquil) % stepSUEn == 0) {
enLJSUnit[mol[j1].inSUnit] += uVal;
}
V_V_S_ADD (mol[j2].ra, -fcVal, dr);
// controlling forces acting on substrate atoms
if (mol[j1].r.z > centUCinZ[0]) {
V_V_S_ADD (force1, fcVal, dr);
} else {
V_V_S_ADD (force2, fcVal, dr);
}
V_V_S_ADD (forceT, fcVal, dr);
} else if ((mol[j1].inChain == -1) && (mol[j1].inSUnit == -2) && (mol[j2].inChain != -1)) {
if (problem == 0) {
fcVal = 4. * 48. * epsTopW * rri3 * ss3_sur * rri3 * ss3_sur * rri; // rep interaction with flatTopW
uVal = 4. * 4. * epsTopW * rri3 * ss3_sur * rri3 * ss3_sur;
} else {
fcVal = 48. * epsTopW * rri3 * ss3_sur * (rri3 * ss3_sur - 0.5) * rri; // rep-attr interaction with flatTopW
uVal = 4. * epsTopW * rri3 * ss3_sur * (rri3 * ss3_sur - 1.);
}
U_LJ_sub += uVal;
uValPP = 0.;
uValPS = uVal;
if ((stepCount > stepEquil) && (stepCount - stepEquil) % stepSUEn == 0) {
enLJSUnit[mol[j1].inSUnit] += uVal;
}
V_V_S_ADD (mol[j2].ra, -fcVal, dr);
} else if ((mol[j1].inChain != -1) && (mol[j2].inChain == -1) && (mol[j2].inSUnit != -2)) {
fcVal = 48. * epsWall * rri3 * ss3_sur * (rri3 * ss3_sur - 0.5) * rri; // interaction with the substrate
uVal = 4. * epsWall * rri3 * ss3_sur * (rri3 * ss3_sur - 1.) - U0_surf;
U_LJ_sub += uVal;
uValPP = 0.;
uValPS = uVal;
if ((stepCount > stepEquil) && (stepCount - stepEquil) % stepSUEn == 0) {
enLJSUnit[mol[j2].inSUnit] += uVal;
}
V_V_S_ADD (mol[j1].ra, fcVal, dr);
// controlling forces acting on substrate atoms
if (mol[j2].r.z > centUCinZ[0]) {
V_V_S_ADD (force1, -fcVal, dr);
} else {
V_V_S_ADD (force2, -fcVal, dr);
}
V_V_S_ADD (forceT, -fcVal, dr);
} else if ((mol[j1].inChain != -1) && (mol[j2].inChain == -1) && (mol[j2].inSUnit == -2)) {
if (problem == 0) {
fcVal = 4. * 48. * epsTopW * rri3 * ss3_sur * rri3 * ss3_sur * rri; // rep interaction with flatTopW
uVal = 4. * 4. * epsTopW * rri3 * ss3_sur * rri3 * ss3_sur;
} else {
fcVal = 48. * epsTopW * rri3 * ss3_sur * (rri3 * ss3_sur - 0.5) * rri; // rep-attr interaction with flatTopW
uVal = 4. * epsTopW * rri3 * ss3_sur * (rri3 * ss3_sur - 1.);
}
U_LJ_sub += uVal;
uValPP = 0.;
uValPS = uVal;
if ((stepCount > stepEquil) && (stepCount - stepEquil) % stepSUEn == 0) {
enLJSUnit[mol[j2].inSUnit] += uVal;
}
V_V_S_ADD (mol[j1].ra, fcVal, dr);
} else {
}
if ((stepCount > stepEquil) && (stepCount - stepEquil) % stepConVal == 0) {
V_DIV (invWid, sizeVelGrid, region);
/* sorting interaction energy for j1 */
V_S_ADD (rs, mol[j1].r, 0.5, region); //shifts coordinates to "positive" region (from 0 to L)
V_MUL (cc, rs, invWid);
c = V_LINEAR (cc, sizeVelGrid);
snapEnGrid[1][c] += 0.5 * uValPP;
snapEnGrid[2][c] += 0.5 * uValPS;
// snapEnGrid[3][c] += 0.5 * produced by thermostat
/* sorting interaction energy for j2 */
V_S_ADD (rs, mol[j2].r, 0.5, region); //shifts coordinates to "positive" region (from 0 to L)
V_MUL (cc, rs, invWid);
c = V_LINEAR (cc, sizeVelGrid);
snapEnGrid[1][c] += 0.5 * uValPP;
snapEnGrid[2][c] += 0.5 * uValPS;
// snapEnGrid[3][c] += 0.5 * produced by thermostat
}
uSum += uVal;
virSum += fcVal * rr;
/* calculating pressure tensor components */
if ((stepCount > stepEquil) && ((stepCount - stepEquil) % stepConVal == 0)) {
secTermX = xx * fcVal;
secTermY = yy * fcVal;
secTermZ = zz * fcVal;
secTermXY = secTermX + secTermY;
/* interacting particles are in the same slab */
if (top == 0) {
histPx[j_max] += secTermX;
histPy[j_max] += secTermY;
// j1 particle is the substrate atom
if (mol[j1].inChain == -1) { // if mol[j1] is an atom of the substrate
histPnW[j_max] += secTermZ;
// histPnW[j_max] -= secTermZ * mol[j2].r.z / dr.z;
histPtW[j_max] += secTermX * mol[j2].r.x / dr.x + secTermY * mol[j2].r.y / dr.y;
}
// j2 particle is the substrate atom
else if (mol[j2].inChain == -1) { // if mol[j2] is an atom of the substrate
histPnW[j_max] += secTermZ;
// histPnW[j_max] += secTermZ * mol[j1].r.z / dr.z;
histPtW[j_max] += secTermX * mol[j1].r.x / dr.x + secTermY * mol[j1].r.y / dr.y;
}
// neither j1 nor j2 are substrate atoms
else { // the interaction happens in the polymer solution (not with the substrate atom)
histPn[j_max] += secTermZ;
histPt[j_max] += secTermXY;
}
}
/* interacting particles are in different slabs */
else {
// treating slab with maximal number
histPx[j_max] += secTermX * dTop * zi;
histPy[j_max] += secTermY * dTop * zi;
if (mol[j1].inChain == -1) {
histPnW[j_max] += secTermZ * dTop * zi;
// histPnW[j_max] += (topSubAtZ + .5 * region.z) * secTermZ * dTop * zi / dr.z; // corr number 1
histPtW[j_max] += (secTermX * mol[j2].r.x / dr.x + secTermY * mol[j2].r.y / dr.y) * dTop * zi;
if (mol[j1].r.z < centUCinZ[0]) {
// histPnW[j_max] -= secTermZ * zi * zi * dTop * 0.5 * gapSurf.z; // corr number 2
}
} else if (mol[j2].inChain == -1) {
histPnW[j_max] += secTermZ * dTop * zi;
// histPnW[j_max] -= (topSubAtZ + .5 * region.z) * secTermZ * dTop * zi / dr.z; // corr number 1
histPtW[j_max] -= (secTermX * mol[j1].r.x / dr.x + secTermY * mol[j1].r.y / dr.y) * dTop * zi;
if (mol[j2].r.z < centUCinZ[0]) {
// histPnW[j_max] += secTermZ * zi * zi * dTop * 0.5 * gapSurf.z; // corr number 2
}
} else {
histPn[j_max] += secTermZ * dTop * zi;
histPt[j_max] += secTermXY * dTop * zi;
}
// treating slab with minimal number
histPx[j_min] += secTermX * dBot * zi;
histPy[j_min] += secTermY * dBot * zi;
if (mol[j1].inChain == -1) {
histPnW[j_min] += secTermZ * dBot * zi;
// histPnW[j_min] += (topSubAtZ + .5 * region.z) * secTermZ * dBot * zi / dr.z; // corr number 1
histPtW[j_min] += (secTermX * mol[j2].r.x / dr.x + secTermY * mol[j2].r.y / dr.y) * dBot * zi;
if (mol[j1].r.z < centUCinZ[0]) {
histPnW[j_min] -= secTermZ * zi * dBot; // corr number 2
}
} else if (mol[j2].inChain == -1) {
histPnW[j_min] += secTermZ * dBot * zi;
// histPnW[j_min] -= (topSubAtZ + .5 * region.z) * secTermZ * dTop * zi / dr.z; // corr number 1
histPtW[j_min] -= (secTermX * mol[j1].r.x / dr.x + secTermY * mol[j1].r.y / dr.y) * dBot * zi;
if (mol[j2].r.z < centUCinZ[0]) {
histPnW[j_min] -= secTermZ * zi * dBot; // corr number 2
}
} else {
histPn[j_min] += secTermZ * dBot * zi;
histPt[j_min] += secTermXY * dBot * zi;
}
// treating slabs between min and max numbers
if (((j_max - j_min) < halfSl) && ((j_max - j_min) > 1)) {
for (j = j_min + 1; j < j_max; j++) {
histPx[j] += secTermX * hSlab * zi;
histPy[j] += secTermY * hSlab * zi;
if (mol[j1].inChain == -1) {
histPnW[j] += secTermZ * hSlab * zi;
// histPnW[j] += (topSubAtZ + .5 * region.z) * secTermZ * hSlab * zi / dr.z; // corr number 1
histPtW[j] += (secTermX * mol[j2].r.x / dr.x + secTermY * mol[j2].r.y / dr.y) * hSlab * zi;
if ((mol[j1].r.z < centUCinZ[0]) && (j < N_high_surf)) {
histPnW[j] -= secTermZ * zi * hSlab; // corr number 2
} else if ((mol[j1].r.z < centUCinZ[0]) && (j == N_high_surf)) {
histPnW[j] -= secTermZ * zi * dTop_high_surf; // corr number 2
} else {
}
} else if (mol[j2].inChain == -1) {
histPnW[j] += secTermZ * hSlab * zi;
// histPnW[j] -= (topSubAtZ + .5 * region.z) * secTermZ * hSlab * zi / dr.z; // corr number 1
histPtW[j] -= (secTermX * mol[j1].r.x / dr.x + secTermY * mol[j1].r.y / dr.y) * hSlab * zi;
if ((mol[j2].r.z < centUCinZ[0]) && (j < N_high_surf)) {
histPnW[j] -= secTermZ * zi * hSlab; // corr number 2
} else if ((mol[j2].r.z < centUCinZ[0]) && (j == N_high_surf)) {
histPnW[j] -= secTermZ * zi * dTop_high_surf; // corr number 2
} else {
}
} else {
histPn[j] += secTermZ * hSlab * zi;
histPt[j] += secTermXY * hSlab * zi;
}
}
}
// when the box has a periodicity in z-direction
/* if (((j_max - j_min) > halfSl) && ((j_max - j_min) < (numSlabs - 1))) {
if (j_min > 0) {
for (j = 0; j < j_min; j++) {
histPt[j] += secTermXY * hSlab * zi;
histPx[j] += secTermX * hSlab * zi;
histPy[j] += secTermY * hSlab * zi;
histPn[j] += secTermZ * hSlab * zi;
}
}
if (j_max < numSlabs - 1) {
for (j = j_max + 1; j < numSlabs; j++) {
histPt[j] += secTermXY * hSlab * zi;
histPx[j] += secTermX * hSlab * zi;
histPy[j] += secTermY * hSlab * zi;
histPn[j] += secTermZ * hSlab * zi;
}
}
}*/
}
}
/* dissipative forces */
omega_r = sqrt(rri) - 1. / rCut; // omega_r / abs (Rij)
V_SUB (dv, mol[j1].rv, mol[j2].rv);
scal = V_DOT (dr, dv);
/* random forces */
zeta = sqrt (12. * 2. * temperature * gamma_d / deltaT);
theta = RandR () - 0.5;
fDispRand = (zeta * theta - gamma_d * scal * omega_r) * omega_r;
if ((mol[j1].inChain != -1) && (mol[j2].inChain != -1)) {
V_V_S_ADD (mol[j1].ra, fDispRand, dr);
V_V_S_ADD (mol[j2].ra, -fDispRand, dr);
} else {
// if (mol[j1].inChain == -1) {
// V_V_S_ADD (mol[j2].ra, -fDispRand, dr);
// } else {
// V_V_S_ADD (mol[j1].ra, fDispRand, dr);
// }
}
}
}
}
}
