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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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78
src/fix_thermal_conductivity.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.
@ -35,7 +35,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
int narg, char **arg) :
int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal fix thermal/conductivity command");
@ -55,7 +55,7 @@ FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
else error->all(FLERR,"Illegal fix thermal/conductivity command");
nbin = atoi(arg[5]);
if (nbin % 2 || nbin <= 2)
if (nbin % 2 || nbin <= 2)
error->all(FLERR,"Illegal fix thermal/conductivity command");
// optional keywords
@ -66,10 +66,10 @@ FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
while (iarg < narg) {
if (strcmp(arg[iarg],"swap") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix thermal/conductivity command");
error->all(FLERR,"Illegal fix thermal/conductivity command");
nswap = atoi(arg[iarg+1]);
if (nswap <= 0)
error->all(FLERR,"Fix thermal/conductivity swap value must be positive");
error->all(FLERR,"Fix thermal/conductivity swap value must be positive");
iarg += 2;
} else error->all(FLERR,"Illegal fix thermal/conductivity command");
}
@ -184,39 +184,39 @@ void FixThermalConductivity::end_of_step()
else if (coord >= boxhi && periodicity) coord -= prd;
if (coord >= slablo_lo && coord < slablo_hi) {
ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) ke *= 0.5*rmass[i];
else ke *= 0.5*mass[type[i]];
if (nlo < nswap || ke > ke_lo[nswap-1]) {
for (insert = nlo-1; insert >= 0; insert--)
if (ke < ke_lo[insert]) break;
insert++;
for (m = nlo-1; m >= insert; m--) {
ke_lo[m+1] = ke_lo[m];
index_lo[m+1] = index_lo[m];
}
ke_lo[insert] = ke;
index_lo[insert] = i;
if (nlo < nswap) nlo++;
}
ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) ke *= 0.5*rmass[i];
else ke *= 0.5*mass[type[i]];
if (nlo < nswap || ke > ke_lo[nswap-1]) {
for (insert = nlo-1; insert >= 0; insert--)
if (ke < ke_lo[insert]) break;
insert++;
for (m = nlo-1; m >= insert; m--) {
ke_lo[m+1] = ke_lo[m];
index_lo[m+1] = index_lo[m];
}
ke_lo[insert] = ke;
index_lo[insert] = i;
if (nlo < nswap) nlo++;
}
}
if (coord >= slabhi_lo && coord < slabhi_hi) {
ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) ke *= 0.5*rmass[i];
else ke *= 0.5*mass[type[i]];
if (nhi < nswap || ke < ke_hi[nswap-1]) {
for (insert = nhi-1; insert >= 0; insert--)
if (ke > ke_hi[insert]) break;
insert++;
for (m = nhi-1; m >= insert; m--) {
ke_hi[m+1] = ke_hi[m];
index_hi[m+1] = index_hi[m];
}
ke_hi[insert] = ke;
index_hi[insert] = i;
if (nhi < nswap) nhi++;
}
ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) ke *= 0.5*rmass[i];
else ke *= 0.5*mass[type[i]];
if (nhi < nswap || ke < ke_hi[nswap-1]) {
for (insert = nhi-1; insert >= 0; insert--)
if (ke > ke_hi[insert]) break;
insert++;
for (m = nhi-1; m >= insert; m--) {
ke_hi[m+1] = ke_hi[m];
index_hi[m+1] = index_hi[m];
}
ke_hi[insert] = ke;
index_hi[insert] = i;
if (nhi < nswap) nhi++;
}
}
}
@ -240,7 +240,7 @@ void FixThermalConductivity::end_of_step()
else mine[0].value = BIG;
if (ihi < nhi) mine[1].value = ke_hi[ihi];
else mine[1].value = BIG;
MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MINLOC,world);
if (all[0].value == BIG || all[1].value == BIG) continue;
@ -272,7 +272,7 @@ void FixThermalConductivity::end_of_step()
eswap -= rbuf[3] * (vcm[0] * (vcm[0] - rbuf[0]) +
vcm[1] * (vcm[1] - rbuf[1]) +
vcm[2] * (vcm[2] - rbuf[2]));
} else if (me == all[0].proc) {
j = index_lo[ilo++];
sbuf[0] = v[j][0];
@ -281,7 +281,7 @@ void FixThermalConductivity::end_of_step()
if (rmass) sbuf[3] = rmass[j];
else sbuf[3] = mass[type[j]];
MPI_Sendrecv(sbuf,4,MPI_DOUBLE,all[1].proc,0,
rbuf,4,MPI_DOUBLE,all[1].proc,0,world,&status);
rbuf,4,MPI_DOUBLE,all[1].proc,0,world,&status);
vcm[0] = (sbuf[3]*sbuf[0] + rbuf[3]*rbuf[0]) / (sbuf[3] + rbuf[3]);
vcm[1] = (sbuf[3]*sbuf[1] + rbuf[3]*rbuf[1]) / (sbuf[3] + rbuf[3]);
vcm[2] = (sbuf[3]*sbuf[2] + rbuf[3]*rbuf[2]) / (sbuf[3] + rbuf[3]);
@ -300,7 +300,7 @@ void FixThermalConductivity::end_of_step()
if (rmass) sbuf[3] = rmass[j];
else sbuf[3] = mass[type[j]];
MPI_Sendrecv(sbuf,4,MPI_DOUBLE,all[0].proc,0,
rbuf,4,MPI_DOUBLE,all[0].proc,0,world,&status);
rbuf,4,MPI_DOUBLE,all[0].proc,0,world,&status);
vcm[0] = (sbuf[3]*sbuf[0] + rbuf[3]*rbuf[0]) / (sbuf[3] + rbuf[3]);
vcm[1] = (sbuf[3]*sbuf[1] + rbuf[3]*rbuf[1]) / (sbuf[3] + rbuf[3]);
vcm[2] = (sbuf[3]*sbuf[2] + rbuf[3]*rbuf[2]) / (sbuf[3] + rbuf[3]);