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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4547 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-08-20 20:43:41 +00:00
parent 52070e6fce
commit 5450680d03
17 changed files with 277 additions and 76 deletions
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143
src/dump_custom.cpp
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@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "dump_custom.h"
@ -37,7 +38,7 @@ enum{ID,MOL,TYPE,MASS,
X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,RADIUS,OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,SPIN,ERADIUS,EVEL,EFORCE,
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
@ -586,6 +587,7 @@ int DumpCustom::count()
} else if (thresh_array[ithresh] == FZ) {
ptr = &atom->f[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == Q) {
if (!atom->q_flag)
error->all("Threshhold for an atom property that isn't allocated");
@ -606,6 +608,7 @@ int DumpCustom::count()
error->all("Threshhold for an atom property that isn't allocated");
ptr = &atom->mu[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == RADIUS) {
if (!atom->radius_flag)
error->all("Threshhold for an atom property that isn't allocated");
@ -641,6 +644,7 @@ int DumpCustom::count()
error->all("Threshhold for an atom property that isn't allocated");
ptr = &atom->angmom[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == QUATW) {
if (!atom->quat_flag)
error->all("Threshhold for an atom property that isn't allocated");
@ -677,6 +681,29 @@ int DumpCustom::count()
ptr = &atom->torque[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == SPIN) {
if (!atom->spin_flag)
error->all("Threshhold for an atom property that isn't allocated");
int *spin = atom->spin;
for (i = 0; i < nlocal; i++) dchoose[i] = spin[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ERADIUS) {
if (!atom->eradius_flag)
error->all("Threshhold for an atom property that isn't allocated");
ptr = atom->eradius;
nstride = 1;
} else if (thresh_array[ithresh] == EVEL) {
if (!atom->evel_flag)
error->all("Threshhold for an atom property that isn't allocated");
ptr = atom->evel;
nstride = 1;
} else if (thresh_array[ithresh] == EFORCE) {
if (!atom->eforce_flag)
error->all("Threshhold for an atom property that isn't allocated");
ptr = atom->eforce;
nstride = 1;
} else if (thresh_array[ithresh] == COMPUTE) {
i = nfield + ithresh;
if (argindex[i] == 0) {
@ -971,6 +998,27 @@ void DumpCustom::parse_fields(int narg, char **arg)
pack_choice[i] = &DumpCustom::pack_tqz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"spin") == 0) {
if (!atom->spin_flag)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_spin;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"eradius") == 0) {
if (!atom->eradius_flag)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_eradius;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"evel") == 0) {
if (!atom->evel_flag)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_evel;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"eforce") == 0) {
if (!atom->evel_flag)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_eforce;
vtype[i] = DOUBLE;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is int between []
@ -1234,10 +1282,12 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"fx") == 0) thresh_array[nthresh] = FX;
else if (strcmp(arg[1],"fy") == 0) thresh_array[nthresh] = FY;
else if (strcmp(arg[1],"fz") == 0) thresh_array[nthresh] = FZ;
else if (strcmp(arg[1],"q") == 0) thresh_array[nthresh] = Q;
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],"radius") == 0) thresh_array[nthresh] = RADIUS;
else if (strcmp(arg[1],"omegax") == 0) thresh_array[nthresh] = OMEGAX;
else if (strcmp(arg[1],"omegay") == 0) thresh_array[nthresh] = OMEGAY;
@ -1245,6 +1295,7 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"angmomx") == 0) thresh_array[nthresh] = ANGMOMX;
else if (strcmp(arg[1],"angmomy") == 0) thresh_array[nthresh] = ANGMOMY;
else if (strcmp(arg[1],"angmomz") == 0) thresh_array[nthresh] = ANGMOMZ;
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;
@ -1252,7 +1303,12 @@ int DumpCustom::modify_param(int narg, char **arg)
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;
else if (strcmp(arg[1],"spin") == 0) thresh_array[nthresh] = SPIN;
else if (strcmp(arg[1],"eradius") == 0) thresh_array[nthresh] = ERADIUS;
else if (strcmp(arg[1],"evel") == 0) thresh_array[nthresh] = EVEL;
else if (strcmp(arg[1],"eforce") == 0) thresh_array[nthresh] = EFORCE;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// must grow field2index and argindex arrays, since access is beyond nfield
@ -2175,3 +2231,86 @@ void DumpCustom::pack_tqz(int n)
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_spin(int n)
{
int *spin = atom->spin;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = spin[i];
n += size_one;
}
}
/* ----------------------------------------------------------------------
different interpretation of electron radius
depending on dynamics vs minimization
------------------------------------------------------------------------- */
void DumpCustom::pack_eradius(int n)
{
double *eradius = atom->eradius;
int *spin = atom->spin;
int nlocal = atom->nlocal;
if (update->whichflag == 1) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = eradius[i];
n += size_one;
}
} else {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
if (spin[i]) buf[n] = exp(eradius[i]);
else buf[n] = 0.0;
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_evel(int n)
{
double *evel = atom->evel;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = evel[i];
n += size_one;
}
}
/* ----------------------------------------------------------------------
different interpretation of electron radial force
depending on dynamics vs minimization
------------------------------------------------------------------------- */
void DumpCustom::pack_eforce(int n)
{
double *eradius = atom->eradius;
double *eforce = atom->eforce;
int *spin = atom->spin;
int nlocal = atom->nlocal;
if (update->whichflag == 1) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = eforce[i];
n += size_one;
}
} else {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
if (spin[i]) buf[n] = eforce[i]/exp(eradius[i]);
else buf[n] = 0.0;
n += size_one;
}
}
}