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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8008 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-04-10 15:02:16 +00:00
parent e75bdb13f0
commit fb1c3d6019
8 changed files with 102 additions and 42 deletions
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2
src/balance.cpp
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@ -32,7 +32,7 @@ enum{NONE,UNIFORM,USER,DYNAMIC};
enum{X,Y,Z};
enum{EXPAND,CONTRACT};
#define BALANCE_DEBUG 1
//#define BALANCE_DEBUG 1
/* ---------------------------------------------------------------------- */

37
src/domain.cpp
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@ -1025,6 +1025,43 @@ void Domain::unmap(double *x, int image, double *y)
}
}
/* ----------------------------------------------------------------------
adjust image flags due to triclinic box flip
flip operation is changing box vectors A,B,C to new A',B',C'
A' = A (A does not change)
B' = B + mA (B shifted by A)
C' = C + pB + nA (C shifted by B and/or A)
this requires the image flags change from (a,b,c) to (a',b',c')
so that x_unwrap for each atom is same before/after
x_unwrap_before = xlocal + aA + bB + cC
x_unwrap_after = xlocal + a'A' + b'B' + c'C'
this requires:
c' = c
b' = b - cp
a' = a - (b-cp)m - cn = a - b'm - cn
in other words, for xy flip, change in x flag depends on current y flag
this is b/c the xy flip dramatically changes which tiled image of
simulation box an unwrapped point maps to
------------------------------------------------------------------------- */
void Domain::image_flip(int m, int n, int p)
{
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
int xbox = (image[i] & 1023) - 512;
int ybox = (image[i] >> 10 & 1023) - 512;
int zbox = (image[i] >> 20) - 512;
ybox -= p*zbox;
xbox -= m*ybox + n*zbox;
image[i] = ((zbox + 512 & 1023) << 20) |
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
}
}
/* ----------------------------------------------------------------------
create a lattice
delete it if style = none

11
src/domain.h
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@ -93,16 +93,17 @@ class Domain : protected Pointers {
virtual void set_local_box();
virtual void reset_box();
virtual void pbc();
void remap(double *, int &);
void remap(double *);
void remap_near(double *, double *);
void unmap(double *, int);
void unmap(double *, int, double *);
int minimum_image_check(double, double, double);
void minimum_image(double &, double &, double &);
void minimum_image(double *);
void closest_image(const double * const, const double * const,
double * const);
void remap(double *, int &);
void remap(double *);
void remap_near(double *, double *);
void unmap(double *, int);
void unmap(double *, int, double *);
void image_flip(int, int, int);
void set_lattice(int, char **);
void add_region(int, char **);
void delete_region(int, char **);

39
src/fix_deform.cpp
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@ -635,13 +635,10 @@ void FixDeform::init()
/* ----------------------------------------------------------------------
box flipped on previous step
do not allow box flip in a non-periodic dimension (can tilt but not flip)
this is b/c the box length will be changed (dramatically) by flip
perform irregular comm to migrate atoms to new procs
reset box tilts for flipped config and create new box in domain
remap to put far-away atoms back into new box
perform irregular on atoms in lamda coords to get atoms to new procs
force reneighboring on next timestep
remap() puts atoms outside the new box back into the new box
image_tilt() adjusts image flags due to box shape change induced by flip
perform irregular on atoms in lamda coords to migrate atoms to new procs
------------------------------------------------------------------------- */
void FixDeform::pre_exchange()
@ -658,6 +655,7 @@ void FixDeform::pre_exchange()
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->image_flip(flipxy,flipxz,flipyz);
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
@ -828,12 +826,13 @@ void FixDeform::end_of_step()
if (varflag) modify->addstep_compute(update->ntimestep + nevery);
// if any tilt ratios exceed 0.5, set flip = 1 & compute new tilt_flip values
// do not flip in x or y if non-periodic
// when yz flips and xy is non-zero, xz must also change
// this is to keep the edge vectors of the flipped shape matrix
// an integer combination of the edge vectors of the unflipped shape matrix
// flip is performed on next timestep before reneighboring
// if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values
// do not flip in x or y if non-periodic (can tilt but not flip)
// this is b/c the box length would be changed (dramatically) by flip
// if yz tilt exceeded, adjust C vector by one B vector
// if xz tilt exceeded, adjust C vector by one A vector
// if xy tilt exceeded, adjust B vector by one A vector
// flip is performed on next timestep, before reneighboring in pre-exchange()
if (triclinic) {
double xprd = set[0].hi_target - set[0].lo_target;
@ -850,36 +849,40 @@ void FixDeform::end_of_step()
set[4].tilt_flip = set[4].tilt_target;
set[5].tilt_flip = set[5].tilt_target;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (set[3].tilt_flip*yprdinv < -0.5) {
set[3].tilt_flip += yprd;
set[4].tilt_flip += set[5].tilt_flip;
flip = 1;
flipyz = 1;
} else if (set[3].tilt_flip*yprdinv > 0.5) {
set[3].tilt_flip -= yprd;
set[4].tilt_flip -= set[5].tilt_flip;
flipy = 1;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (set[4].tilt_flip*xprdinv < -0.5) {
set[4].tilt_flip += xprd;
flip = 1;
flipxz = 1;
}
if (set[4].tilt_flip*xprdinv > 0.5) {
set[4].tilt_flip -= xprd;
flip = 1;
flipxz = -1;
}
if (set[5].tilt_flip*xprdinv < -0.5) {
set[5].tilt_flip += xprd;
flip = 1;
flipxy = 1;
}
if (set[5].tilt_flip*xprdinv > 0.5) {
set[5].tilt_flip -= xprd;
flip = 1;
flipxy = -1;
}
}
flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) next_reneighbor = update->ntimestep + 1;
}
}

2
src/fix_deform.h
View File

@ -38,7 +38,7 @@ class FixDeform : public Fix {
private:
int triclinic,scaleflag;
int flip,flipx,flipy;
int flip,flipxy,flipxz,flipyz;
double *h_rate,*h_ratelo;
int varflag; // 1 if VARIABLE option is used, 0 if not
int kspace_flag; // 1 if KSpace invoked, 0 if not

42
src/fix_nh.cpp
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@ -85,7 +85,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (domain->xz != 0.0) scalexz = 1;
}
// Set fixed-point to default = center of cell
// set fixed-point to default = center of cell
fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
@ -116,7 +116,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
error->all(FLERR,"Target temperature for fix nvt/npt/nph cannot be 0.0");
error->all(FLERR,
"Target temperature for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
@ -2137,12 +2138,16 @@ void FixNH::nh_omega_dot()
}
/* ----------------------------------------------------------------------
if any tilt ratios exceed 0.5, set flip = 1 & compute new tilt_flip values
do not flip in x or y if non-periodic
when yz flips and xy is non-zero, xz must also change
this is to keep the edge vectors of the flipped shape matrix
an integer combination of the edge vectors of the unflipped shape matrix
perform irregular on atoms in lamda coords to get atoms to new procs
if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values
do not flip in x or y if non-periodic (can tilt but not flip)
this is b/c the box length would be changed (dramatically) by flip
if yz tilt exceeded, adjust C vector by one B vector
if xz tilt exceeded, adjust C vector by one A vector
if xy tilt exceeded, adjust B vector by one A vector
if any flip occurs, create new box in domain
remap() puts atoms outside the new box back into the new box
image_tilt() adjusts image flags due to box shape change induced by flip
perform irregular on atoms in lamda coords to migrate atoms to new procs
------------------------------------------------------------------------- */
void FixNH::pre_exchange()
@ -2156,37 +2161,41 @@ void FixNH::pre_exchange()
double xtiltmax = (0.5+DELTAFLIP)*xprd;
double ytiltmax = (0.5+DELTAFLIP)*yprd;
int flip = 0;
int flipxy,flipxz,flipyz;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (domain->yz < -ytiltmax) {
flip = 1;
domain->yz += yprd;
domain->xz += domain->xy;
flipyz = 1;
} else if (domain->yz >= ytiltmax) {
flip = 1;
domain->yz -= yprd;
domain->xz -= domain->xy;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (domain->xz < -xtiltmax) {
flip = 1;
domain->xz += xprd;
flipxz = 1;
} else if (domain->xz >= xtiltmax) {
flip = 1;
domain->xz -= xprd;
flipxz = -1;
}
if (domain->xy < -xtiltmax) {
flip = 1;
domain->xy += xprd;
flipxy = 1;
} else if (domain->xy >= xtiltmax) {
flip = 1;
domain->xy -= xprd;
flipxy = -1;
}
}
int flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) {
domain->set_global_box();
domain->set_local_box();
@ -2195,7 +2204,8 @@ void FixNH::pre_exchange()
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->image_flip(flipxy,flipxz,flipyz);
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
domain->lamda2x(atom->nlocal);

9
src/lattice.cpp
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@ -313,6 +313,15 @@ Lattice::~Lattice()
int Lattice::orthogonal()
{
double a = orientx[0]*orienty[0] + orientx[1]*orienty[1] +
orientx[2]*orienty[2];
double b = orienty[0]*orientz[0] + orienty[1]*orientz[1] +
orienty[2]*orientz[2];
double c = orientx[0]*orientz[0] + orientx[1]*orientz[1] +
orientx[2]*orientz[2];
printf("ABC %g %g %g\n",a,b,c);
if (orientx[0]*orienty[0] + orientx[1]*orienty[1] +
orientx[2]*orienty[2]) return 0;
if (orienty[0]*orientz[0] + orienty[1]*orientz[1] +

2
src/set.cpp
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@ -497,7 +497,7 @@ void Set::set(int keyword)
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
// set dipole moment