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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6251 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-05-30 15:46:44 +00:00
parent 575de169b9
commit 405d127522
6 changed files with 124 additions and 56 deletions
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92
src/dump_custom.cpp
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@ -32,18 +32,19 @@
using namespace LAMMPS_NS;
// customize by adding keyword
// same list as in compute_property.cpp, also customize that command
// also customize compute_atom_property.cpp
enum{ID,MOL,TYPE,MASS,
enum{ID,MOL,TYPE,ELEMENT,MASS,
X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,
XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,MU,RADIUS,OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
enum{INT,DOUBLE,STRING};
#define INVOKED_PERATOM 8
@ -97,6 +98,11 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
choose = NULL;
dchoose = NULL;
// element names
ntypes = atom->ntypes;
typenames = NULL;
// setup format strings
vformat = new char*[size_one];
@ -106,7 +112,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < size_one; i++) {
if (vtype[i] == INT) format_default = strcat(format_default,"%d ");
else format_default = strcat(format_default,"%g ");
else if (vtype[i] == DOUBLE) format_default = strcat(format_default,"%g ");
else if (vtype[i] == STRING) strcat(format_default,"%s ");
vformat[i] = NULL;
}
@ -153,6 +160,11 @@ DumpCustom::~DumpCustom()
memory->destroy(choose);
memory->destroy(dchoose);
if (typenames) {
for (int i = 1; i <= ntypes; i++) delete [] typenames[i];
delete [] typenames;
}
for (int i = 0; i < size_one; i++) delete [] vformat[i];
delete [] vformat;
@ -172,6 +184,16 @@ void DumpCustom::init_style()
format = new char[n];
strcpy(format,str);
// default for element names = C
if (typenames == NULL) {
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = new char[2];
strcpy(typenames[itype],"C");
}
}
// tokenize the format string and add space at end of each format element
char *ptr;
@ -429,6 +451,11 @@ int DumpCustom::count()
for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ELEMENT) {
int *type = atom->type;
for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == MASS) {
if (atom->rmass) {
ptr = atom->rmass;
@ -581,7 +608,8 @@ int DumpCustom::count()
double boxylo = domain->boxlo[1];
double invyprd = 1.0/domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][1] - boxylo) * invyprd + (image[i] >> 10 & 1023) - 512;
dchoose[i] =
(x[i][1] - boxylo) * invyprd + (image[i] >> 10 & 1023) - 512;
ptr = dchoose;
nstride = 1;
@ -698,6 +726,13 @@ int DumpCustom::count()
error->all("Threshhold for an atom property that isn't allocated");
ptr = atom->radius;
nstride = 1;
} else if (thresh_array[ithresh] == DIAMETER) {
if (!atom->radius_flag)
error->all("Threshhold for an atom property that isn't allocated");
double *radius = atom->radius;
for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == OMEGAX) {
if (!atom->omega_flag)
error->all("Threshhold for an atom property that isn't allocated");
@ -880,7 +915,9 @@ void DumpCustom::write_text(int n, double *mybuf)
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
m++;
}
fprintf(fp,"\n");
@ -908,6 +945,9 @@ void DumpCustom::parse_fields(int narg, char **arg)
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"element") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
vtype[i] = STRING;
} else if (strcmp(arg[iarg],"mass") == 0) {
pack_choice[i] = &DumpCustom::pack_mass;
vtype[i] = DOUBLE;
@ -1017,6 +1057,11 @@ void DumpCustom::parse_fields(int narg, char **arg)
error->all("Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_radius;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all("Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_diameter;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all("Dumping an atom property that isn't allocated");
@ -1271,6 +1316,24 @@ int DumpCustom::modify_param(int narg, char **arg)
}
return 2;
} else if (strcmp(arg[0],"element") == 0) {
if (narg != ntypes+1)
error->all("Dump modify element names do not match atom types");
if (typenames) {
for (int i = 1; i <= ntypes; i++) delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
int n = strlen(arg[itype]) + 1;
typenames[itype] = new char[n];
strcpy(typenames[itype],arg[itype]);
}
return ntypes+1;
} else if (strcmp(arg[0],"thresh") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) {
@ -1362,6 +1425,7 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"mu") == 0) thresh_array[nthresh] = MU;
else if (strcmp(arg[1],"radius") == 0) thresh_array[nthresh] = RADIUS;
else if (strcmp(arg[1],"diameter") == 0) thresh_array[nthresh] = DIAMETER;
else if (strcmp(arg[1],"omegax") == 0) thresh_array[nthresh] = OMEGAX;
else if (strcmp(arg[1],"omegay") == 0) thresh_array[nthresh] = OMEGAY;
else if (strcmp(arg[1],"omegaz") == 0) thresh_array[nthresh] = OMEGAZ;
@ -2236,6 +2300,20 @@ void DumpCustom::pack_radius(int n)
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_diameter(int n)
{
double *radius = atom->radius;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = 2.0*radius[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_omegax(int n)
{
double **omega = atom->omega;