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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8551 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-08-07 16:12:48 +00:00
parent 435a693fd8
commit be1e06897b
8 changed files with 81 additions and 23 deletions
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41
src/domain.cpp
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@ -65,6 +65,8 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
boundary[2][0] = boundary[2][1] = 0;
triclinic = 0;
tiltsmall = 1;
boxlo[0] = boxlo[1] = boxlo[2] = -0.5;
boxhi[0] = boxhi[1] = boxhi[2] = 0.5;
xy = xz = yz = 0.0;
@ -135,17 +137,20 @@ void Domain::set_initial_box()
if (boxlo[0] >= boxhi[0] || boxlo[1] >= boxhi[1] || boxlo[2] >= boxhi[2])
error->one(FLERR,"Box bounds are invalid");
// error check on triclinic tilt factors
if (triclinic) {
if (domain->dimension == 2 && (xz != 0.0 || yz != 0.0))
error->all(FLERR,"Cannot skew triclinic box in z for 2d simulation");
if (fabs(xy/(boxhi[0]-boxlo[0])) > 0.5)
error->all(FLERR,"Triclinic box skew is too large");
if (fabs(xz/(boxhi[0]-boxlo[0])) > 0.5)
error->all(FLERR,"Triclinic box skew is too large");
if (fabs(yz/(boxhi[1]-boxlo[1])) > 0.5)
// error check or warning on triclinic tilt factors
if (triclinic) {
if ((fabs(xy/(boxhi[0]-boxlo[0])) > 0.5) ||
(fabs(xz/(boxhi[0]-boxlo[0])) > 0.5) ||
(fabs(yz/(boxhi[1]-boxlo[1])) > 0.5)) {
if (tiltsmall)
error->all(FLERR,"Triclinic box skew is too large");
else if (comm->me == 0)
error->warning(FLERR,"Triclinic box skew is large");
}
}
// set small based on box size and SMALL
@ -1277,6 +1282,26 @@ void Domain::set_boundary(int narg, char **arg, int flag)
}
}
/* ----------------------------------------------------------------------
set domain attributes
------------------------------------------------------------------------- */
void Domain::set_box(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal box command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"tilt") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal box command");
if (strcmp(arg[iarg+1],"small") == 0) tiltsmall = 1;
else if (strcmp(arg[iarg+1],"large") == 0) tiltsmall = 0;
else error->all(FLERR,"Illegal box command");
iarg += 2;
} else error->all(FLERR,"Illegal box command");
}
}
/* ----------------------------------------------------------------------
print box info, orthogonal or triclinic
------------------------------------------------------------------------- */

2
src/domain.h
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@ -36,6 +36,7 @@ class Domain : protected Pointers {
// 3 = shrink-wrap non-per w/ min
int triclinic; // 0 = orthog box, 1 = triclinic
int tiltsmall; // 1 if limit tilt, else 0
// orthogonal box
double xprd,yprd,zprd; // global box dimensions
@ -111,6 +112,7 @@ class Domain : protected Pointers {
void delete_region(int, char **);
int find_region(char *);
void set_boundary(int, char **, int);
void set_box(int, char **);
void print_box(const char *);
void boundary_string(char *);

20
src/fix_deform.cpp
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@ -354,7 +354,8 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// reneighboring only forced if flips can occur due to shape changes
if (set[3].style || set[4].style || set[5].style) force_reneighbor = 1;
if (flipflag && (set[3].style || set[4].style || set[5].style))
force_reneighbor = 1;
next_reneighbor = -1;
nrigid = 0;
@ -565,23 +566,27 @@ void FixDeform::init()
// an integer combination of the edge vectors of the unflipped shape matrix
// VARIABLE for yz is error, since no way to calculate if box flip occurs
// WIGGLE lo/hi flip test is on min/max oscillation limit, not tilt_stop
// only trigger actual errors if flipflag is set
if (set[3].style && set[5].style) {
int flag = 0;
double lo,hi;
if (set[3].style == VARIABLE)
if (flipflag && set[3].style == VARIABLE)
error->all(FLERR,"Fix deform cannot use yz variable with xy");
if (set[3].style == WIGGLE) {
lo = set[3].tilt_min;
hi = set[3].tilt_max;
} else lo = hi = set[3].tilt_stop;
if (flipflag) {
if (lo/(set[1].hi_start-set[1].lo_start) < -0.5 ||
hi/(set[1].hi_start-set[1].lo_start) > 0.5) flag = 1;
if (set[1].style) {
if (lo/(set[1].hi_stop-set[1].lo_stop) < -0.5 ||
hi/(set[1].hi_stop-set[1].lo_stop) > 0.5) flag = 1;
}
if (flag) error->all(FLERR,"Fix deform is changing yz too much with xy");
if (flag)
error->all(FLERR,"Fix deform is changing yz too much with xy");
}
}
// set domain->h_rate values for use by domain and other fixes/computes
@ -838,7 +843,7 @@ void FixDeform::end_of_step()
// check yz first since it may change xz, then xz check comes after
// flip is performed on next timestep, before reneighboring in pre-exchange()
if (triclinic) {
if (triclinic && flipflag) {
double xprd = set[0].hi_target - set[0].lo_target;
double yprd = set[1].hi_target - set[1].lo_target;
double xprdinv = 1.0 / xprd;
@ -960,6 +965,7 @@ void FixDeform::options(int narg, char **arg)
remapflag = X_REMAP;
scaleflag = 1;
flipflag = 1;
int iarg = 0;
while (iarg < narg) {
@ -976,6 +982,12 @@ void FixDeform::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix deform command");
iarg += 2;
} else if (strcmp(arg[iarg],"flip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"yes") == 0) flipflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) flipflag = 0;
else error->all(FLERR,"Illegal fix deform command");
iarg += 2;
} else error->all(FLERR,"Illegal fix deform command");
}
}

2
src/fix_deform.h
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@ -37,7 +37,7 @@ class FixDeform : public Fix {
void end_of_step();
private:
int triclinic,scaleflag;
int triclinic,scaleflag,flipflag;
int flip,flipxy,flipxz,flipyz;
double *h_rate,*h_ratelo;
int varflag; // 1 if VARIABLE option is used, 0 if not

13
src/fix_nh.cpp
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@ -75,6 +75,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
eta_mass_flag = 1;
omega_mass_flag = 0;
etap_mass_flag = 0;
flipflag = 1;
// turn on tilt factor scaling, whenever applicable
@ -308,6 +309,12 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
else if (strcmp(arg[iarg+1],"no") == 0) scaleyz = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"flip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) flipflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) flipflag = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"fixedpoint") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
fixedpoint[0] = atof(arg[iarg+1]);
@ -437,8 +444,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// reneighboring only forced if flips can occur due to shape changes
if (p_flag[3] || p_flag[4] || p_flag[5]) force_reneighbor = 1;
if (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0)
if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5])) force_reneighbor = 1;
if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0))
force_reneighbor = 1;
// convert input periods to frequencies
@ -2199,7 +2206,7 @@ void FixNH::pre_exchange()
double xprd = domain->xprd;
double yprd = domain->yprd;
// flip is triggered when tilt exceeds 0.5 by an amount DELTAFLIP
// flip is only triggered when tilt exceeds 0.5 by DELTAFLIP
// this avoids immediate re-flipping due to tilt oscillations
double xtiltmax = (0.5+DELTAFLIP)*xprd;

3
src/fix_nh.h
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@ -112,8 +112,9 @@ class FixNH : public Fix {
int scaleyz; // 1 if yz scaled with lz
int scalexz; // 1 if xz scaled with lz
int scalexy; // 1 if xy scaled with ly
int flipflag; // 1 if box flips are invoked as needed
double fixedpoint[3]; // Location of dilation fixed-point
double fixedpoint[3]; // location of dilation fixed-point
void couple();
void remap();

10
src/input.cpp
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@ -450,6 +450,7 @@ int Input::execute_command()
else if (!strcmp(command,"bond_coeff")) bond_coeff();
else if (!strcmp(command,"bond_style")) bond_style();
else if (!strcmp(command,"boundary")) boundary();
else if (!strcmp(command,"box")) box();
else if (!strcmp(command,"communicate")) communicate();
else if (!strcmp(command,"compute")) compute();
else if (!strcmp(command,"compute_modify")) compute_modify();
@ -954,6 +955,15 @@ void Input::boundary()
/* ---------------------------------------------------------------------- */
void Input::box()
{
if (domain->box_exist)
error->all(FLERR,"Box command after simulation box is defined");
domain->set_box(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::communicate()
{
comm->set(narg,arg);

1
src/input.h
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@ -71,6 +71,7 @@ class Input : protected Pointers {
void bond_coeff();
void bond_style();
void boundary();
void box();
void communicate();
void compute();
void compute_modify();