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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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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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126
src/fix_adapt.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.
@ -84,13 +84,13 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
adapt[nadapt].pparam = new char[n];
strcpy(adapt[nadapt].pparam,arg[iarg+2]);
force->bounds(arg[iarg+3],atom->ntypes,
adapt[nadapt].ilo,adapt[nadapt].ihi);
adapt[nadapt].ilo,adapt[nadapt].ihi);
force->bounds(arg[iarg+4],atom->ntypes,
adapt[nadapt].jlo,adapt[nadapt].jhi);
adapt[nadapt].jlo,adapt[nadapt].jhi);
if (strstr(arg[iarg+5],"v_") == arg[iarg+5]) {
n = strlen(&arg[iarg+5][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
n = strlen(&arg[iarg+5][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 6;
@ -98,9 +98,9 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = KSPACE;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
int n = strlen(&arg[iarg+1][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
@ -108,13 +108,13 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0) {
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+2][2]);
int n = strlen(&arg[iarg+2][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+2][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 3;
@ -205,28 +205,28 @@ void FixAdapt::init()
ad->pdim = 2;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
if (ad->pdim == 2) ad->array = (double **) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
if (!pair->check_ijtype(i,j,ad->pstyle))
error->all(FLERR,"Fix adapt type pair range is not valid for "
"pair hybrid sub-style");
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
if (!pair->check_ijtype(i,j,ad->pstyle))
error->all(FLERR,"Fix adapt type pair range is not valid for "
"pair hybrid sub-style");
}
} else if (ad->which == KSPACE) {
if (force->kspace == NULL)
error->all(FLERR,"Fix adapt kspace style does not exist");
if (force->kspace == NULL)
error->all(FLERR,"Fix adapt kspace style does not exist");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->aparam == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
}
}
}
@ -237,8 +237,8 @@ void FixAdapt::init()
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
}
}
}
@ -281,22 +281,22 @@ void FixAdapt::change_settings()
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
double value = input->variable->compute_equal(ad->ivar);
// set global scalar or type pair array values
if (ad->which == PAIR) {
if (ad->pdim == 0) {
if (scaleflag) *ad->scalar = value * ad->scalar_orig;
else *ad->scalar = value;
if (scaleflag) *ad->scalar = value * ad->scalar_orig;
else *ad->scalar = value;
} else if (ad->pdim == 2) {
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value*ad->array_orig[i][j];
else
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value;
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value*ad->array_orig[i][j];
else
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value;
}
// set kspace scale factor
@ -310,29 +310,29 @@ void FixAdapt::change_settings()
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
int mflag = 0;
if (atom->rmass_flag) mflag = 1;
double density;
int mflag = 0;
if (atom->rmass_flag) mflag = 1;
double density;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (mflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
radius[i] = 0.5*value;
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = 0.5*value;
rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
}
if (mflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
radius[i] = 0.5*value;
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = 0.5*value;
rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
}
}
}
}
@ -357,9 +357,9 @@ void FixAdapt::restore_settings()
if (ad->which == PAIR) {
if (ad->pdim == 0) *ad->scalar = ad->scalar_orig;
else if (ad->pdim == 2) {
for (int i = ad->ilo; i <= ad->ihi; i++)
for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = ad->array_orig[i][j];
for (int i = ad->ilo; i <= ad->ihi; i++)
for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = ad->array_orig[i][j];
}
} else if (ad->which == KSPACE) {