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Modified remap() function to include full tensor product for barostatting tilted boxes 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4341 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2010-06-25 16:51:02 +00:00
parent 20df3d8445
commit 5fadc65fc3
2 changed files with 108 additions and 76 deletions
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177
src/fix_nh.cpp
View File

@ -567,8 +567,6 @@ void FixNH::setup(int vflag)
{
// initialize some quantities that were not available earlier
if (mtk_flag) mtk_factor = 1.0 + 1.0/atom->natoms;
else mtk_factor = 1.0;
tdof = temperature->dof;
// t_target is used by compute_scalar(), even for NPH
@ -639,9 +637,6 @@ void FixNH::setup(int vflag)
boltz*t_target) / etap_mass[ich];
}
// compute appropriately coupled elements of mvv_current
if (mtk_flag) couple_ke();
}
}
@ -681,7 +676,6 @@ void FixNH::initial_integrate(int vflag)
}
couple();
pressure->addstep(update->ntimestep+1);
if (mtk_flag) couple_ke();
}
if (pstat_flag) {
@ -726,7 +720,6 @@ void FixNH::final_integrate()
else pressure->compute_vector();
couple();
pressure->addstep(update->ntimestep+1);
if (mtk_flag) couple_ke();
}
if (pstat_flag) nh_omega_dot();
@ -750,7 +743,7 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// outermost level - update eta_dot and omega_dot, apply to v, remap box
// outermost level - update eta_dot and omega_dot, apply to v
// all other levels - NVE update of v
// x,v updates only performed for atoms in group
@ -786,7 +779,6 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
}
couple();
pressure->addstep(update->ntimestep+1);
if (mtk_flag) couple_ke();
}
if (pstat_flag) {
@ -869,37 +861,6 @@ void FixNH::couple()
}
}
/* ---------------------------------------------------------------------- */
void FixNH::couple_ke()
{
double *tensor = temperature->vector;
if (pstyle == ISO)
mvv_current[0] = mvv_current[1] = mvv_current[2] =
tdof * boltz * t_current/dimension;
else if (pcouple == XYZ) {
double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
mvv_current[0] = mvv_current[1] = mvv_current[2] = ave;
} else if (pcouple == XY) {
double ave = 0.5 * (tensor[0] + tensor[1]);
mvv_current[0] = mvv_current[1] = ave;
mvv_current[2] = tensor[2];
} else if (pcouple == YZ) {
double ave = 0.5 * (tensor[1] + tensor[2]);
mvv_current[1] = mvv_current[2] = ave;
mvv_current[0] = tensor[0];
} else if (pcouple == XZ) {
double ave = 0.5 * (tensor[0] + tensor[2]);
mvv_current[0] = mvv_current[2] = ave;
mvv_current[1] = tensor[1];
} else {
mvv_current[0] = tensor[0];
mvv_current[1] = tensor[1];
mvv_current[2] = tensor[2];
}
}
/* ----------------------------------------------------------------------
change box size
remap all atoms or fix group atoms depending on allremap flag
@ -914,6 +875,7 @@ void FixNH::remap()
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *h = domain->h;
// omega is not used, except for book-keeping
@ -934,15 +896,41 @@ void FixNH::remap()
// reset global and local box to new size/shape
// This operation corresponds to applying the
// translate and scale operations
// corresponding to the solution of the following ODE:
//
// h_dot = omega_dot * h
//
// where h_dot, omega_dot and h are all upper-triangular
// 3x3 tensors. In Voigt notation, the elements of the
// RHS product tensor are:
// h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
//
// Ordering of operations preserves time symmetry.
double dto2 = dto/2.0;
double dto4 = dto/4.0;
double dto8 = dto/8.0;
if (pstyle == TRICLINIC) {
domain->yz += domain->zprd*dilation[3];
domain->xz += domain->zprd*dilation[4];
domain->xy += domain->yprd*dilation[5];
if (domain->yz < -0.5*domain->yprd || domain->yz > 0.5*domain->yprd ||
domain->xz < -0.5*domain->xprd || domain->xz > 0.5*domain->xprd ||
domain->xy < -0.5*domain->xprd || domain->xy > 0.5*domain->xprd)
error->all("fix npt/nph has tilted box beyond 45 degrees");
h[4] *= exp(dto8*omega_dot[0]);
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
h[3] *= exp(dto4*omega_dot[1]);
h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= exp(dto4*omega_dot[1]);
h[5] *= exp(dto4*omega_dot[0]);
h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= exp(dto4*omega_dot[0]);
h[4] *= exp(dto8*omega_dot[0]);
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
}
for (i = 0; i < 3; i++) {
@ -950,11 +938,39 @@ void FixNH::remap()
oldlo = domain->boxlo[i];
oldhi = domain->boxhi[i];
ctr = 0.5 * (oldlo + oldhi);
domain->boxlo[i] = (oldlo-ctr)*dilation[i] + ctr;
domain->boxhi[i] = (oldhi-ctr)*dilation[i] + ctr;
domain->boxlo[i] = (oldlo-ctr)*exp(dto*omega_dot[i]) + ctr;
domain->boxhi[i] = (oldhi-ctr)*exp(dto*omega_dot[i]) + ctr;
}
}
if (pstyle == TRICLINIC) {
h[4] *= exp(dto8*omega_dot[0]);
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
h[3] *= exp(dto4*omega_dot[1]);
h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= exp(dto4*omega_dot[1]);
h[5] *= exp(dto4*omega_dot[0]);
h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= exp(dto4*omega_dot[0]);
h[4] *= exp(dto8*omega_dot[0]);
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= exp(dto8*omega_dot[0]);
domain->yz = h[3];
domain->xz = h[4];
domain->xy = h[5];
if (domain->yz < -0.5*domain->yprd || domain->yz > 0.5*domain->yprd ||
domain->xz < -0.5*domain->xprd || domain->xz > 0.5*domain->xprd ||
domain->xy < -0.5*domain->xprd || domain->xy > 0.5*domain->xprd)
error->all("fix npt/nph has tilted box beyond 45 degrees");
}
domain->set_global_box();
domain->set_local_box();
@ -1566,11 +1582,16 @@ void FixNH::nhc_press_integrate()
void FixNH::nh_v_press()
{
double factor[3];
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -1578,9 +1599,12 @@ void FixNH::nh_v_press()
v[i][1] *= factor[1];
v[i][2] *= factor[2];
if (pstyle == TRICLINIC) {
v[i][0] += v[i][1]*factor[5] + v[i][2]*factor[4];
v[i][1] += v[i][2]*factor[3];
v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
v[i][1] += -dthalf*v[i][2]*omega_dot[3];
}
v[i][0] *= factor[0];
v[i][1] *= factor[1];
v[i][2] *= factor[2];
}
}
} else if (which == BIAS) {
@ -1591,9 +1615,12 @@ void FixNH::nh_v_press()
v[i][1] *= factor[1];
v[i][2] *= factor[2];
if (pstyle == TRICLINIC) {
v[i][0] += v[i][1]*factor[5] + v[i][2]*factor[4];
v[i][1] += v[i][2]*factor[3];
v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
v[i][1] += -dthalf*v[i][2]*omega_dot[3];
}
v[i][0] *= factor[0];
v[i][1] *= factor[1];
v[i][2] *= factor[2];
temperature->restore_bias(i,v[i]);
}
}
@ -1844,38 +1871,50 @@ void FixNH::compute_press_target()
}
/* ----------------------------------------------------------------------
update omega_dot, omega, dilation
update omega_dot, omega
-----------------------------------------------------------------------*/
void FixNH::nh_omega_dot()
{
double mtk_term;
double f_omega,volume;
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
else volume = domain->xprd*domain->yprd;
if (deviatoric_flag) compute_deviatoric();
for (int i = 0; i < 3; i++) {
mtk_term1 = 0.0;
if (mtk_flag)
if (pstyle == ISO) {
mtk_term1 = tdof * boltz * t_current;
mtk_term1 /= pdim * atom->natoms;
} else {
double *mvv_current = temperature->vector;
for (int i = 0; i < 3; i++)
if (p_flag[i])
mtk_term1 += mvv_current[i];
mtk_term1 /= pdim * atom->natoms;
}
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
if (mtk_flag) mtk_term = mvv_current[i]/(atom->natoms*volume) * nktv2p;
else mtk_term = 0.0;
f_omega = (p_current[i]-p_hydro+mtk_term)*volume /
(omega_mass[i] * nktv2p);
f_omega = (p_current[i]-p_hydro)*volume /
(omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= pdrag_factor;
}
factor[i] = exp(-dthalf*omega_dot[i]*mtk_factor);
dilation[i] = exp(dto*omega_dot[i]);
mtk_term2 = 0.0;
if (mtk_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i])
mtk_term2 += omega_dot[i];
mtk_term2 /= pdim * atom->natoms;
}
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++) {
if (p_flag[i]) {
f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
if (deviatoric_flag)
@ -1883,10 +1922,6 @@ void FixNH::nh_omega_dot()
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= pdrag_factor;
}
factor[i] = -dthalf*omega_dot[i];
dilation[i] = dto*omega_dot[i];
}
}
}

7
src/fix_nh.h
View File

@ -55,10 +55,9 @@ class FixNH : public Fix {
double p_freq[6],p_target[6];
double omega[6],omega_dot[6];
double omega_mass[6];
double p_current[6],dilation[6];
double p_current[6];
double drag,tdrag_factor; // drag factor on particle thermostat
double pdrag_factor; // drag factor on barostat
double factor[6]; // velocity scaling due to barostat
int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigid; // number of rigid fixes
int *rfix; // indices of rigid fixes
@ -83,8 +82,6 @@ class FixNH : public Fix {
int mtk_flag; // 0 if using Hoover barostat
int pdim; // number of barostatted dims
double mvv_current[3]; // diagonal of KE tensor
double mtk_factor; // MTK factor
double p_freq_max; // maximum barostat frequency
double p_hydro; // hydrostatic target pressure
@ -96,9 +93,9 @@ class FixNH : public Fix {
int deviatoric_flag; // 0 if target stress tensor is hydrostatic
double h0_inv[6]; // h_inv of reference (zero strain) box
int nreset_h0; // interval for resetting h0
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
void couple();
void couple_ke();
void remap();
void nhc_temp_integrate();
void nhc_press_integrate();