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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-06-20 13:17:59 +00:00
parent bde732bced
commit aaed6ebc33
131 changed files with 4277 additions and 2222 deletions
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128
src/dump_custom.cpp
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@ -31,7 +31,8 @@ using namespace LAMMPS_NS;
enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,TQX,TQY,TQZ,
Q,MUX,MUY,MUZ,
QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
EPAIR,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
COMPUTE};
enum{LT,LE,GT,GE,EQ,NEQ};
@ -405,6 +406,18 @@ int DumpCustom::count()
} else if (thresh_array[ithresh] == MUZ) {
ptr = &atom->mu[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == QUATW) {
ptr = &atom->quat[0][0];
nstride = 4;
} else if (thresh_array[ithresh] == QUATI) {
ptr = &atom->quat[0][1];
nstride = 4;
} else if (thresh_array[ithresh] == QUATJ) {
ptr = &atom->quat[0][2];
nstride = 4;
} else if (thresh_array[ithresh] == QUATK) {
ptr = &atom->quat[0][3];
nstride = 4;
} else if (thresh_array[ithresh] == TQX) {
ptr = &atom->torque[0][0];
nstride = 3;
@ -455,27 +468,29 @@ int DumpCustom::count()
}
}
// unselect atoms that don't meet threshhold criterion
value = thresh_value[ithresh];
if (thresh_op[ithresh] == GE) {
if (thresh_op[ithresh] == LT) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == GT) {
} else if (thresh_op[ithresh] == LE) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == LE) {
} else if (thresh_op[ithresh] == GT) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == LT) {
} else if (thresh_op[ithresh] == GE) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < value) {
choose[i] = 0;
@ -483,13 +498,13 @@ int DumpCustom::count()
}
} else if (thresh_op[ithresh] == EQ) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == value) {
if (choose[i] && *ptr != value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == NEQ) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != value) {
if (choose[i] && *ptr == value) {
choose[i] = 0;
nmine--;
}
@ -645,6 +660,27 @@ void DumpCustom::parse_fields(int narg, char **arg)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"quatw") == 0) {
if (atom->quat == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_quatw;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"quati") == 0) {
if (atom->quat == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_quati;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"quatj") == 0) {
if (atom->quat == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_quatj;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"quatk") == 0) {
if (atom->quat == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_quatk;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (atom->torque == NULL)
error->all("Dumping an atom quantity that isn't allocated");
@ -825,10 +861,8 @@ int DumpCustom::modify_param(int narg, char **arg)
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) iregion = -1;
else {
for (iregion = 0; iregion < domain->nregion; iregion++)
if (strcmp(arg[1],domain->regions[iregion]->id) == 0) break;
if (iregion == domain->nregion)
error->all("Dump_modify region ID does not exist");
iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all("Dump_modify region ID does not exist");
}
return 2;
@ -896,6 +930,10 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"mux") == 0) thresh_array[nthresh] = MUX;
else if (strcmp(arg[1],"muy") == 0) thresh_array[nthresh] = MUY;
else if (strcmp(arg[1],"muz") == 0) thresh_array[nthresh] = MUZ;
else if (strcmp(arg[1],"quatw") == 0) thresh_array[nthresh] = QUATW;
else if (strcmp(arg[1],"quati") == 0) thresh_array[nthresh] = QUATI;
else if (strcmp(arg[1],"quatj") == 0) thresh_array[nthresh] = QUATJ;
else if (strcmp(arg[1],"quatk") == 0) thresh_array[nthresh] = QUATK;
else if (strcmp(arg[1],"tqx") == 0) thresh_array[nthresh] = TQX;
else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY;
else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ;
@ -1013,12 +1051,12 @@ int DumpCustom::modify_param(int narg, char **arg)
// set operation type of threshhold
if (strcmp(arg[2],">=") == 0) thresh_op[nthresh] = LT;
else if (strcmp(arg[2],">") == 0) thresh_op[nthresh] = LE;
else if (strcmp(arg[2],"<=") == 0) thresh_op[nthresh] = GT;
else if (strcmp(arg[2],"<") == 0) thresh_op[nthresh] = GE;
else if (strcmp(arg[2],"=") == 0) thresh_op[nthresh] = NEQ;
else if (strcmp(arg[2],"<>") == 0) thresh_op[nthresh] = EQ;
if (strcmp(arg[2],"<") == 0) thresh_op[nthresh] = LT;
else if (strcmp(arg[2],"<=") == 0) thresh_op[nthresh] = LE;
else if (strcmp(arg[2],">") == 0) thresh_op[nthresh] = GT;
else if (strcmp(arg[2],">=") == 0) thresh_op[nthresh] = GE;
else if (strcmp(arg[2],"==") == 0) thresh_op[nthresh] = EQ;
else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ;
else error->all("Invalid dump_modify threshhold operator");
// set threshhold value
@ -1441,6 +1479,62 @@ void DumpCustom::pack_muz(int n)
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_quatw(int n)
{
double **quat = atom->quat;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = quat[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_quati(int n)
{
double **quat = atom->quat;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = quat[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_quatj(int n)
{
double **quat = atom->quat;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = quat[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_quatk(int n)
{
double **quat = atom->quat;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = quat[i][3];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_tqx(int n)
{
double **torque = atom->torque;