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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8216 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-01 23:29:31 +00:00
parent fe568c6697
commit 17be5191be
10 changed files with 66 additions and 44 deletions
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7
src/GRANULAR/fix_wall_gran.cpp
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@ -49,6 +49,10 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/gran requires atom style sphere");
// set time_depend so that history will be preserved correctly
// across multiple runs via laststep setting in granular pair styles
// same as fix shear/history
restart_peratom = 1;
create_attribute = 1;
time_depend = 1;
@ -150,7 +154,8 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic))
error->all(FLERR,"Cannot use wall in periodic dimension");
if (wiggle && wshear) error->all(FLERR,"Cannot wiggle and shear fix wall/gran");
if (wiggle && wshear)
error->all(FLERR,"Cannot wiggle and shear fix wall/gran");
if (wiggle && wallstyle == ZCYLINDER && axis != 2)
error->all(FLERR,"Invalid wiggle direction for fix wall/gran");
if (wshear && wallstyle == XPLANE && axis == 0)

13
src/MC/fix_gcmc.cpp
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@ -68,7 +68,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (nexchanges < 0) error->all(FLERR,"Illegal fix GCMC command");
if (nmcmoves < 0) error->all(FLERR,"Illegal fix GCMC command");
if (seed <= 0) error->all(FLERR,"Illegal fix GCMC command");
if (reservoir_temperature < 0.0) error->all(FLERR,"Illegal fix GCMC command");
if (reservoir_temperature < 0.0)
error->all(FLERR,"Illegal fix GCMC command");
if (displace < 0.0) error->all(FLERR,"Illegal fix GCMC command");
// compute beta, lambda, sigma, and the zz factor
@ -175,13 +176,16 @@ void FixGCMC::init()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,"Fix GCMC may delete atom with non-zero molecule ID");
error->warning(FLERR,
"Fix GCMC may delete atom with non-zero molecule ID");
}
if (molflag && atom->molecule_flag == 0)
error->all(FLERR,"Fix GCMC molecule command requires atom attribute molecule");
error->all(FLERR,
"Fix GCMC molecule command requires atom attribute molecule");
if (molflag != 0) error->all(FLERR,"Fix GCMC molecule feature does not yet work");
if (molflag != 0)
error->all(FLERR,"Fix GCMC molecule feature does not yet work");
if (force->pair->single_enable == 0)
error->all(FLERR,"Fix GCMC incompatible with given pair_style");
@ -303,7 +307,6 @@ void FixGCMC::attempt_move()
nmove_successes += 1.0;
comm->borders();
}
}
/* ----------------------------------------------------------------------

4
src/SHOCK/fix_append_atoms.cpp
View File

@ -216,9 +216,7 @@ int FixAppendAtoms::setmask()
void FixAppendAtoms::initial_integrate(int vflag)
{
if (update->ntimestep % freq == 0) {
next_reneighbor = update->ntimestep;
}
if (update->ntimestep % freq == 0) next_reneighbor = update->ntimestep;
}
/* ---------------------------------------------------------------------- */

67
src/SHOCK/fix_wall_piston.cpp
View File

@ -38,7 +38,6 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
force_reneighbor = 1;
next_reneighbor = -1;
box_change = 1;
time_depend = 1;
if (narg < 4) error->all(FLERR,"Illegal fix wall/piston command");
@ -54,19 +53,25 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
rampNL5flag = 0;
x0 = y0 = z0 = vx = vy = vz = 0.0;
xloflag = xhiflag = yloflag = yhiflag = zloflag = zhiflag = 0;
int iarg = 0;
iarg = 3;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"xlo") == 0) { error->all(FLERR,"Fix wall/piston command only available at zlo");
} else if (strcmp(arg[iarg],"ylo") == 0) { error->all(FLERR,"Fix wall/piston command only available at zlo");
} else if (strcmp(arg[iarg],"zlo") == 0) {
if (strcmp(arg[iarg],"xlo") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"ylo") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"zlo") == 0) {
zloflag = 1;
iarg++;
if (domain->boundary[2][0] != 2) error->all(FLERR,"Must shrink-wrap piston boundary");
} else if (strcmp(arg[iarg],"xhi") == 0) { error->all(FLERR,"Fix wall/piston command only available at zlo");
} else if (strcmp(arg[iarg],"yhi") == 0) { error->all(FLERR,"Fix wall/piston command only available at zlo");
} else if (strcmp(arg[iarg],"zhi") == 0) { error->all(FLERR,"Fix wall/piston command only available at zlo");
} else if (strcmp(arg[iarg],"vel") == 0) {
if (domain->boundary[2][0] != 2)
error->all(FLERR,"Must shrink-wrap piston boundary");
} else if (strcmp(arg[iarg],"xhi") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"yhi") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"zhi") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/piston command");
vx = atof(arg[iarg+1]);
vy = atof(arg[iarg+2]);
@ -124,7 +129,8 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal fix wall/piston command");
}
if (vx < 0.0 || vy < 0.0 || vz < 0.0) error->all(FLERR,"Illegal fix wall/piston velocity");
if (vx < 0.0 || vy < 0.0 || vz < 0.0)
error->all(FLERR,"Illegal fix wall/piston velocity");
if ((xloflag || xhiflag) && domain->xperiodic)
error->all(FLERR,"Cannot use wall in periodic dimension");
if ((yloflag || yhiflag) && domain->yperiodic)
@ -153,7 +159,8 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
z0 *= zscale;
roughdist *= zscale;
if (rampflag || rampNL1flag || rampNL2flag || rampNL3flag || rampNL4flag || rampNL5flag) {
if (rampflag || rampNL1flag || rampNL2flag || rampNL3flag ||
rampNL4flag || rampNL5flag) {
maxvx = vx;
maxvy = vy;
maxvz = vz;
@ -165,9 +172,9 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
int FixWallPiston::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
mask |= INITIAL_INTEGRATE;
return mask;
}
@ -209,20 +216,26 @@ void FixWallPiston::post_integrate()
angfreq = MY_2PI / (0.5 * tott);
if (zloflag) {
zlo = z0 + paccelz * (0.5*tt + 1.0/(angfreq*angfreq) - 1.0/(angfreq*angfreq)*cos(angfreq*t));
zlo = z0 + paccelz * (0.5*tt + 1.0/(angfreq*angfreq) -
1.0/(angfreq*angfreq)*cos(angfreq*t));
vz = paccelz * (t + 1.0/angfreq*sin(angfreq*t));
}
else { error->all(FLERR,"NL ramp in wall/piston only implemented in zlo for now"); }
else error->all(FLERR,
"NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL2flag) {
paccelz = maxvz / tott;
angfreq = 3.0*MY_2PI / tott;
if (zloflag) {
zlo = z0 + paccelz * (0.5*tt + 4.0/(3.0*angfreq*angfreq)*(1.0-cos(angfreq*t)) + 1.0/(6.0*angfreq*angfreq)*(1.0-cos(2.0*angfreq*t)));
vz = paccelz * (t + 4.0/(3.0*angfreq)*sin(angfreq*t) + 1.0/(3.0*angfreq)*sin(2.0*angfreq*t));
zlo = z0 + paccelz * (0.5*tt + 4.0/(3.0*angfreq*angfreq)*
(1.0-cos(angfreq*t)) +
1.0/(6.0*angfreq*angfreq)*(1.0-cos(2.0*angfreq*t)));
vz = paccelz * (t + 4.0/(3.0*angfreq)*sin(angfreq*t) +
1.0/(3.0*angfreq)*sin(2.0*angfreq*t));
}
else { error->all(FLERR,"NL ramp in wall/piston only implemented in zlo for now"); }
else error->all(FLERR,
"NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL3flag) {
paccelz = maxvz / tott;
@ -231,7 +244,8 @@ void FixWallPiston::post_integrate()
zlo = z0 + paccelz*tott*tott/2.5 * (t2p5 );
vz = paccelz * tott * (t1p5 );
}
else { error->all(FLERR,"NL ramp in wall/piston only implemented in zlo for now"); }
else error->all(FLERR,
"NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL4flag) {
paccelz = maxvz / tott;
@ -240,7 +254,8 @@ void FixWallPiston::post_integrate()
zlo = z0 + paccelz/tott/3.0 * (ttt);
vz = paccelz / tott * (tt);
}
else { error->all(FLERR,"NL ramp in wall/piston only implemented in zlo for now"); }
else error->all(FLERR,
"NL ramp in wall/piston only implemented in zlo for now");
}
else if (rampNL5flag) {
paccelz = maxvz / tott;
@ -249,7 +264,8 @@ void FixWallPiston::post_integrate()
zlo = z0 + paccelz/tott/tott/4.0 * (tttt);
vz = paccelz / tott / tott * (ttt);
}
else { error->all(FLERR,"NL ramp in wall/piston only implemented in zlo for now"); }
else error->all(FLERR,
"NL ramp in wall/piston only implemented in zlo for now");
}
else {
if (zloflag) { zlo = z0 + vz * t; }
@ -273,8 +289,10 @@ void FixWallPiston::post_integrate()
if (mask[i] & groupbit) {
roughoff = 0.0;
if (roughflag) {
roughoff += roughdist*fabs((x[i][0] - domain->boxlo[0])/(domain->boxhi[0]-domain->boxlo[0])-0.5);
roughoff += roughdist*fabs((x[i][1] - domain->boxlo[1])/(domain->boxhi[1]-domain->boxlo[1])-0.5);
roughoff += roughdist*fabs((x[i][0] - domain->boxlo[0])/
(domain->boxhi[0]-domain->boxlo[0])-0.5);
roughoff += roughdist*fabs((x[i][1] - domain->boxlo[1])/
(domain->boxhi[1]-domain->boxlo[1])-0.5);
}
if (zloflag && x[i][2] < zlo - roughoff) {
x[i][2] = 2.0 * (zlo - roughoff) - x[i][2];
@ -326,5 +344,4 @@ void FixWallPiston::post_integrate()
}
}
}
}

4
src/SRD/fix_wall_srd.cpp
View File

@ -156,11 +156,11 @@ FixWallSRD::FixWallSRD(LAMMPS *lmp, int narg, char **arg) :
if (dimflag[0] + dimflag[1] + dimflag[2] > 1) overlap = 1;
else overlap = 0;
// set time_depend and varflag if any wall positions are variable
// set varflag if any wall positions are variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) time_depend = varflag = 1;
if (wallstyle[m] == VARIABLE) varflag = 1;
laststep = -1;
}

2
src/USER-CUDA/fix_gravity_cuda.cpp
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@ -53,8 +53,6 @@ FixGravityCuda::FixGravityCuda(LAMMPS *lmp, int narg, char **arg) :
if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
time_depend = 1;
magnitude = atof(arg[3]);
if (strcmp(arg[4],"chute") == 0) {

2
src/fix_dt_reset.cpp
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@ -41,6 +41,8 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 7) error->all(FLERR,"Illegal fix dt/reset command");
// set time_depend, else elapsed time accumulation can be messed up
time_depend = 1;
scalar_flag = 1;
vector_flag = 1;

1
src/fix_restrain.cpp
View File

@ -51,7 +51,6 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
time_depend = 1;
// parse args

4
src/fix_wall.cpp
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@ -152,11 +152,11 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
}
}
// set time_depend and varflag if any wall positions are variable
// set varflag if any wall positions are variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) time_depend = varflag = 1;
if (wallstyle[m] == VARIABLE) varflag = 1;
eflag = 0;
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;

4
src/fix_wall_reflect.cpp
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@ -133,11 +133,11 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
}
}
// set time_depend and varflag if any wall positions are variable
// set varflag if any wall positions are variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) time_depend = varflag = 1;
if (wallstyle[m] == VARIABLE) varflag = 1;
}
/* ---------------------------------------------------------------------- */