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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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232
src/change_box.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -44,12 +44,12 @@ void ChangeBox::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
if (domain->box_exist == 0)
error->all(FLERR,"Change_box command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal change_box command");
if (modify->nfix_restart_peratom)
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot change_box after "
"reading restart file with per-atom info");
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n");
@ -72,7 +72,7 @@ void ChangeBox::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
strcmp(arg[iarg],"z") == 0) {
strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = XYZ;
if (strcmp(arg[iarg],"x") == 0) ops[nops].dim = X;
@ -80,45 +80,45 @@ void ChangeBox::command(int narg, char **arg)
else if (strcmp(arg[iarg],"z") == 0) ops[nops].dim = Z;
if (dimension == 2 && ops[nops].dim == Z)
error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = FINAL;
ops[nops].flo = atof(arg[iarg+2]);
ops[nops].fhi = atof(arg[iarg+3]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 4;
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = FINAL;
ops[nops].flo = atof(arg[iarg+2]);
ops[nops].fhi = atof(arg[iarg+3]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = DELTA;
ops[nops].dlo = atof(arg[iarg+2]);
ops[nops].dhi = atof(arg[iarg+3]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 4;
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = DELTA;
ops[nops].dlo = atof(arg[iarg+2]);
ops[nops].dhi = atof(arg[iarg+3]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"scale") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = SCALE;
ops[nops].scale = atof(arg[iarg+2]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 3;
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = SCALE;
ops[nops].scale = atof(arg[iarg+2]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
if (nops == 0 || ops[nops-1].style != XYZ ||
ops[nops].dim == ops[nops-1].dim)
error->all(FLERR,"Change_box volume used incorrectly");
if (ops[nops-1].vdim2 >= 0)
error->all(FLERR,"Change_box volume used incorrectly");
else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
else ops[nops-1].vdim1 = ops[nops].dim;
iarg += 2;
if (nops == 0 || ops[nops-1].style != XYZ ||
ops[nops].dim == ops[nops-1].dim)
error->all(FLERR,"Change_box volume used incorrectly");
if (ops[nops-1].vdim2 >= 0)
error->all(FLERR,"Change_box volume used incorrectly");
else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
else ops[nops-1].vdim1 = ops[nops].dim;
iarg += 2;
} else error->all(FLERR,"Illegal change_box command");
} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
strcmp(arg[iarg],"yz") == 0) {
strcmp(arg[iarg],"yz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = TILT;
if (strcmp(arg[iarg],"xy") == 0) ops[nops].dim = XY;
@ -126,20 +126,20 @@ void ChangeBox::command(int narg, char **arg)
else if (strcmp(arg[iarg],"yz") == 0) ops[nops].dim = YZ;
if (dimension == 2 && (ops[nops].dim == XZ || ops[nops].dim == YZ))
error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = FINAL;
ops[nops].ftilt = atof(arg[iarg+2]);
nops++;
iarg += 3;
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = FINAL;
ops[nops].ftilt = atof(arg[iarg+2]);
nops++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = DELTA;
ops[nops].dtilt = atof(arg[iarg+2]);
nops++;
iarg += 3;
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = DELTA;
ops[nops].dtilt = atof(arg[iarg+2]);
nops++;
iarg += 3;
} else error->all(FLERR,"Illegal change_box command");
} else if (strcmp(arg[iarg],"boundary") == 0) {
@ -216,85 +216,85 @@ void ChangeBox::command(int narg, char **arg)
else volume = domain->xprd * domain->yprd * domain->zprd;
if (ops[i].flavor == FINAL) {
domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo;
domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi;
if (ops[i].vdim1 >= 0)
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo;
domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi;
if (ops[i].vdim1 >= 0)
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[i].flavor == DELTA) {
domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo;
domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi;
if (ops[i].vdim1 >= 0)
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo;
domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi;
if (ops[i].vdim1 >= 0)
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[i].flavor == SCALE) {
double mid = 0.5 *
(domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]);
double delta = domain->boxlo[ops[i].dim] - mid;
domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta;
delta = domain->boxhi[ops[i].dim] - mid;
domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta;
if (ops[i].vdim1 >= 0)
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
double mid = 0.5 *
(domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]);
double delta = domain->boxlo[ops[i].dim] - mid;
domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta;
delta = domain->boxhi[ops[i].dim] - mid;
domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta;
if (ops[i].vdim1 >= 0)
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
}
} else if (ops[i].style == TILT) {
if (domain->triclinic == 0)
error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
if (ops[i].flavor == FINAL) {
if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt;
else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt;
else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt;
else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt;
else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[i].flavor == DELTA) {
if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt;
else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt;
else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt;
else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt;
else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
}
} else if (ops[i].style == BOUNDARY) {
domain->set_boundary(3,&arg[ops[i].boundindex],1);
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,
"Cannot change box z boundary to "
"nonperiodic for a 2d simulation");
error->all(FLERR,
"Cannot change box z boundary to "
"nonperiodic for a 2d simulation");
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
} else if (ops[i].style == ORTHO) {
if (domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0)
error->all(FLERR,
"Cannot change box to orthogonal when tilt is non-zero");
error->all(FLERR,
"Cannot change box to orthogonal when tilt is non-zero");
if (output->ndump)
error->all(FLERR,
"Cannot change box ortho/triclinic with dumps defined");
error->all(FLERR,
"Cannot change box ortho/triclinic with dumps defined");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->no_change_box)
error->all(FLERR,
"Cannot change box ortho/triclinic with "
"certain fixes defined");
if (modify->fix[i]->no_change_box)
error->all(FLERR,
"Cannot change box ortho/triclinic with "
"certain fixes defined");
domain->triclinic = 0;
domain->set_initial_box();
domain->set_global_box();
@ -303,13 +303,13 @@ void ChangeBox::command(int narg, char **arg)
} else if (ops[i].style == TRICLINIC) {
if (output->ndump)
error->all(FLERR,
"Cannot change box ortho/triclinic with dumps defined");
error->all(FLERR,
"Cannot change box ortho/triclinic with dumps defined");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->no_change_box)
error->all(FLERR,
"Cannot change box ortho/triclinic with "
"certain fixes defined");
if (modify->fix[i]->no_change_box)
error->all(FLERR,
"Cannot change box ortho/triclinic with "
"certain fixes defined");
domain->triclinic = 1;
domain->set_lamda_box();
domain->set_initial_box();
@ -329,14 +329,14 @@ void ChangeBox::command(int narg, char **arg)
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i],boxlo,h_inv);
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i],boxlo,h_inv);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
save_box_state();
}
@ -374,8 +374,8 @@ void ChangeBox::command(int narg, char **arg)
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}