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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7871 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-03-01 15:43:39 +00:00
parent a410531401
commit 4d2eae8344
2 changed files with 84 additions and 86 deletions
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167
src/KSPACE/ewald.cpp
View File

@ -159,7 +159,7 @@ void Ewald::init()
setup();
// final RMS accuracy
// final RMS accuracy
double lprx = rms(kxmax,xprd,natoms,q2);
double lpry = rms(kymax,yprd,natoms,q2);
@ -167,7 +167,7 @@ void Ewald::init()
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
// stats
if (comm->me == 0) {
@ -606,9 +606,6 @@ void Ewald::coeffs()
int k,l,m;
double sqk,vterm;
double unitkx = unitk[0];
double unitky = unitk[1];
double unitkz = unitk[2];
double g_ewald_sq_inv = 1.0 / (g_ewald*g_ewald);
double preu = 4.0*MY_PI/volume;
@ -617,17 +614,17 @@ void Ewald::coeffs()
// (k,0,0), (0,l,0), (0,0,m)
for (m = 1; m <= kmax; m++) {
sqk = (m*unitkx) * (m*unitkx);
sqk = (m*unitk[0]) * (m*unitk[0]);
if (sqk <= gsqmx) {
kxvecs[kcount] = m;
kyvecs[kcount] = 0;
kzvecs[kcount] = 0;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*m*ug[kcount];
eg[kcount][0] = 2.0*unitk[0]*m*ug[kcount];
eg[kcount][1] = 0.0;
eg[kcount][2] = 0.0;
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0 + vterm*(unitkx*m)*(unitkx*m);
vg[kcount][0] = 1.0 + vterm*(unitk[0]*m)*(unitk[0]*m);
vg[kcount][1] = 1.0;
vg[kcount][2] = 1.0;
vg[kcount][3] = 0.0;
@ -635,25 +632,25 @@ void Ewald::coeffs()
vg[kcount][5] = 0.0;
kcount++;
}
sqk = (m*unitky) * (m*unitky);
sqk = (m*unitk[1]) * (m*unitk[1]);
if (sqk <= gsqmx) {
kxvecs[kcount] = 0;
kyvecs[kcount] = m;
kzvecs[kcount] = 0;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 0.0;
eg[kcount][1] = 2.0*unitky*m*ug[kcount];
eg[kcount][1] = 2.0*unitk[1]*m*ug[kcount];
eg[kcount][2] = 0.0;
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0;
vg[kcount][1] = 1.0 + vterm*(unitky*m)*(unitky*m);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*m)*(unitk[1]*m);
vg[kcount][2] = 1.0;
vg[kcount][3] = 0.0;
vg[kcount][4] = 0.0;
vg[kcount][5] = 0.0;
kcount++;
}
sqk = (m*unitkz) * (m*unitkz);
sqk = (m*unitk[2]) * (m*unitk[2]);
if (sqk <= gsqmx) {
kxvecs[kcount] = 0;
kyvecs[kcount] = 0;
@ -661,11 +658,11 @@ void Ewald::coeffs()
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 0.0;
eg[kcount][1] = 0.0;
eg[kcount][2] = 2.0*unitkz*m*ug[kcount];
eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0;
vg[kcount][1] = 1.0;
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = 0.0;
vg[kcount][4] = 0.0;
vg[kcount][5] = 0.0;
@ -677,20 +674,20 @@ void Ewald::coeffs()
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
sqk = (unitkx*k) * (unitkx*k) + (unitky*l) * (unitky*l);
sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l);
if (sqk <= gsqmx) {
kxvecs[kcount] = k;
kyvecs[kcount] = l;
kzvecs[kcount] = 0;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][1] = 2.0*unitky*l*ug[kcount];
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = 0.0;
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0;
vg[kcount][3] = vterm*unitkx*k*unitky*l;
vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
vg[kcount][4] = 0.0;
vg[kcount][5] = 0.0;
kcount++;
@ -699,13 +696,13 @@ void Ewald::coeffs()
kyvecs[kcount] = -l;
kzvecs[kcount] = 0;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][1] = -2.0*unitky*l*ug[kcount];
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = 0.0;
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0;
vg[kcount][3] = -vterm*unitkx*k*unitky*l;
vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
vg[kcount][4] = 0.0;
vg[kcount][5] = 0.0;
kcount++;;
@ -717,22 +714,22 @@ void Ewald::coeffs()
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
sqk = (unitky*l) * (unitky*l) + (unitkz*m) * (unitkz*m);
sqk = (unitk[1]*l) * (unitk[1]*l) + (unitk[2]*m) * (unitk[2]*m);
if (sqk <= gsqmx) {
kxvecs[kcount] = 0;
kyvecs[kcount] = l;
kzvecs[kcount] = m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 0.0;
eg[kcount][1] = 2.0*unitky*l*ug[kcount];
eg[kcount][2] = 2.0*unitkz*m*ug[kcount];
eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0;
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = 0.0;
vg[kcount][4] = 0.0;
vg[kcount][5] = vterm*unitky*l*unitkz*m;
vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
kcount++;
kxvecs[kcount] = 0;
@ -740,14 +737,14 @@ void Ewald::coeffs()
kzvecs[kcount] = -m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 0.0;
eg[kcount][1] = 2.0*unitky*l*ug[kcount];
eg[kcount][2] = -2.0*unitkz*m*ug[kcount];
eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
vg[kcount][0] = 1.0;
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = 0.0;
vg[kcount][4] = 0.0;
vg[kcount][5] = -vterm*unitky*l*unitkz*m;
vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
kcount++;
}
}
@ -757,21 +754,21 @@ void Ewald::coeffs()
for (k = 1; k <= kxmax; k++) {
for (m = 1; m <= kzmax; m++) {
sqk = (unitkx*k) * (unitkx*k) + (unitkz*m) * (unitkz*m);
sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[2]*m) * (unitk[2]*m);
if (sqk <= gsqmx) {
kxvecs[kcount] = k;
kyvecs[kcount] = 0;
kzvecs[kcount] = m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = 0.0;
eg[kcount][2] = 2.0*unitkz*m*ug[kcount];
eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0;
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = 0.0;
vg[kcount][4] = vterm*unitkx*k*unitkz*m;
vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
vg[kcount][5] = 0.0;
kcount++;
@ -779,14 +776,14 @@ void Ewald::coeffs()
kyvecs[kcount] = 0;
kzvecs[kcount] = -m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = 0.0;
eg[kcount][2] = -2.0*unitkz*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0;
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = 0.0;
vg[kcount][4] = -vterm*unitkx*k*unitkz*m;
vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
vg[kcount][5] = 0.0;
kcount++;
}
@ -798,68 +795,68 @@ void Ewald::coeffs()
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
sqk = (unitkx*k) * (unitkx*k) + (unitky*l) * (unitky*l) +
(unitkz*m) * (unitkz*m);
sqk = (unitk[0]*k) * (unitk[0]*k) + (unitk[1]*l) * (unitk[1]*l) +
(unitk[2]*m) * (unitk[2]*m);
if (sqk <= gsqmx) {
kxvecs[kcount] = k;
kyvecs[kcount] = l;
kzvecs[kcount] = m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][1] = 2.0*unitky*l*ug[kcount];
eg[kcount][2] = 2.0*unitkz*m*ug[kcount];
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
vterm = -2.0*(1.0/sqk + 0.25*g_ewald_sq_inv);
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][3] = vterm*unitkx*k*unitky*l;
vg[kcount][4] = vterm*unitkx*k*unitkz*m;
vg[kcount][5] = vterm*unitky*l*unitkz*m;
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
kcount++;
kxvecs[kcount] = k;
kyvecs[kcount] = -l;
kzvecs[kcount] = m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][1] = -2.0*unitky*l*ug[kcount];
eg[kcount][2] = 2.0*unitkz*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][3] = -vterm*unitkx*k*unitky*l;
vg[kcount][4] = vterm*unitkx*k*unitkz*m;
vg[kcount][5] = -vterm*unitky*l*unitkz*m;
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = 2.0*unitk[2]*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
vg[kcount][4] = vterm*unitk[0]*k*unitk[2]*m;
vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
kcount++;
kxvecs[kcount] = k;
kyvecs[kcount] = l;
kzvecs[kcount] = -m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][1] = 2.0*unitky*l*ug[kcount];
eg[kcount][2] = -2.0*unitkz*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][3] = vterm*unitkx*k*unitky*l;
vg[kcount][4] = -vterm*unitkx*k*unitkz*m;
vg[kcount][5] = -vterm*unitky*l*unitkz*m;
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = 2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = vterm*unitk[0]*k*unitk[1]*l;
vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
vg[kcount][5] = -vterm*unitk[1]*l*unitk[2]*m;
kcount++;
kxvecs[kcount] = k;
kyvecs[kcount] = -l;
kzvecs[kcount] = -m;
ug[kcount] = preu*exp(-0.25*sqk*g_ewald_sq_inv)/sqk;
eg[kcount][0] = 2.0*unitkx*k*ug[kcount];
eg[kcount][1] = -2.0*unitky*l*ug[kcount];
eg[kcount][2] = -2.0*unitkz*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitkx*k)*(unitkx*k);
vg[kcount][1] = 1.0 + vterm*(unitky*l)*(unitky*l);
vg[kcount][2] = 1.0 + vterm*(unitkz*m)*(unitkz*m);
vg[kcount][3] = -vterm*unitkx*k*unitky*l;
vg[kcount][4] = -vterm*unitkx*k*unitkz*m;
vg[kcount][5] = vterm*unitky*l*unitkz*m;
eg[kcount][0] = 2.0*unitk[0]*k*ug[kcount];
eg[kcount][1] = -2.0*unitk[1]*l*ug[kcount];
eg[kcount][2] = -2.0*unitk[2]*m*ug[kcount];
vg[kcount][0] = 1.0 + vterm*(unitk[0]*k)*(unitk[0]*k);
vg[kcount][1] = 1.0 + vterm*(unitk[1]*l)*(unitk[1]*l);
vg[kcount][2] = 1.0 + vterm*(unitk[2]*m)*(unitk[2]*m);
vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
vg[kcount][4] = -vterm*unitk[0]*k*unitk[2]*m;
vg[kcount][5] = vterm*unitk[1]*l*unitk[2]*m;
kcount++;;
}
}

3
src/REPLICA/verlet_split.cpp
View File

@ -445,8 +445,9 @@ void VerletSplit::rk_setup()
// KSpace procs need to acquire ghost atoms and map all their atoms
// map_clear() call is in lieu of comm->exchange() which performs map_clear
// borders() call acquires ghost atoms and maps them
// NOTE: don't atom coords need to be communicated here before borders() ??
// NOTE: do atom coords need to be communicated here before borders() call?
// could do this by calling r2k_comm() here and not again from run()
// except that forward_comm() in r2k_comm() is wrong
if (tip4p_flag) {
//r2k_comm();