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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-10-30 20:04:06 +00:00
parent 0aa77408f8
commit 354e20f431
1219 changed files with 10111 additions and 10111 deletions
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28
src/MISC/fix_deposit.cpp
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@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_deposit.h"
#include "atom.h"
#include "atom_vec.h"
@ -107,17 +107,17 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix deposit molecule must have atom types");
if (ntype+onemols[i]->ntypes <= 0 ||
if (ntype+onemols[i]->ntypes <= 0 ||
ntype+onemols[i]->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix deposit mol command");
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemols[i]->check_attributes(0);
// fix deposit uses geoemetric center of molecule for insertion
onemols[i]->compute_center();
}
}
@ -253,7 +253,7 @@ void FixDeposit::init()
// for finite size spherical particles:
// warn if near < 2 * maxrad of existing and inserted particles
// since may lead to overlaps
// if inserted molecule does not define diameters,
// if inserted molecule does not define diameters,
// use AtomVecSphere::create_atom() default radius = 0.5
if (atom->radius_flag) {
@ -482,7 +482,7 @@ void FixDeposit::pre_exchange()
domain->x2lamda(coords[m],lamda);
newcoord = lamda;
} else newcoord = coords[m];
flag = 0;
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
@ -496,7 +496,7 @@ void FixDeposit::pre_exchange()
if (comm->mysplit[2][1] == 1.0 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
}
}
} else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) {
if (comm->layout != LAYOUT_TILED) {
if (comm->myloc[1] == comm->procgrid[1]-1 &&
@ -524,7 +524,7 @@ void FixDeposit::pre_exchange()
atom->v[n][0] = vnew[0];
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
if (mode == MOLECULE)
if (mode == MOLECULE)
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
modify->create_attribute(n);
}
@ -668,9 +668,9 @@ void FixDeposit::options(int narg, char **arg)
if (mode != MOLECULE) error->all(FLERR,"Illegal fix deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
for (int i = 1; i < nmol; i++)
for (int i = 1; i < nmol; i++)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]);
if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
@ -711,13 +711,13 @@ void FixDeposit::options(int narg, char **arg)
globalflag = 0;
lo = force->numeric(FLERR,arg[iarg+1]);
hi = force->numeric(FLERR,arg[iarg+2]);
deltasq = force->numeric(FLERR,arg[iarg+3]) *
deltasq = force->numeric(FLERR,arg[iarg+3]) *
force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"near") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
nearsq = force->numeric(FLERR,arg[iarg+1]) *
nearsq = force->numeric(FLERR,arg[iarg+1]) *
force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"attempt") == 0) {