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Added xsu, ysu, zsu to dump custom and dump cfg 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6044 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2011-04-29 23:40:14 +00:00
parent 21de807010
commit 7c04f95ce0
3 changed files with 254 additions and 13 deletions
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59
src/dump_cfg.cpp
View File

@ -30,6 +30,8 @@
#include "memory.h"
#include "error.h"
#define UNWRAPEXPAND 10.0
using namespace LAMMPS_NS;
enum{INT,DOUBLE}; // same as in dump_custom.cpp
@ -41,10 +43,20 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 10 ||
strcmp(arg[5],"id") != 0 || strcmp(arg[6],"type") != 0 ||
strcmp(arg[7],"xs") != 0 || strcmp(arg[8],"ys") != 0 ||
strcmp(arg[9],"zs") != 0)
error->all("Dump cfg arguments must start with 'id type xs ys zs'");
(strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
(strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
(strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0)
)
error->all("Dump cfg arguments must start with 'id type xs ys zs' or 'id type xsu ysu zsu'");
if (strcmp(arg[7],"xs") == 0)
if (strcmp(arg[8],"ysu") == 0 || strcmp(arg[9],"zsu") == 0)
error->all("Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
else unwrapflag = 0;
else if (strcmp(arg[8],"ys") == 0 || strcmp(arg[9],"zs") == 0)
error->all("Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
else unwrapflag = 1;
ntypes = atom->ntypes;
typenames = NULL;
@ -189,7 +201,9 @@ void DumpCFG::write_header(bigint n)
// special handling for atom style peri
// use average volume of particles to scale particles to mimic C atoms
// scale box dimension to sc lattice for C with sigma = 1.44 Angstroms
// Special handling for unwrapped coordinates
double scale;
if (atom->peri_flag) {
int nlocal = atom->nlocal;
@ -199,9 +213,9 @@ void DumpCFG::write_header(bigint n)
MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
if (atom->natoms) vave /= atom->natoms;
if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0);
else scale = 1.0;
} else scale = 1.0;
} else if (unwrapflag == 1) scale = UNWRAPEXPAND;
else scale = 1.0;
if (me == 0 || multiproc) {
char str[64];
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
@ -261,6 +275,8 @@ void DumpCFG::write_data(int n, double *mybuf)
// write data lines in rbuf to file after transfer is done
double unwrap_coord;
if (nlines == nchosen) {
for (itype = 1; itype <= ntypes; itype++) {
for (i = 0; i < nchosen; i++)
@ -271,11 +287,30 @@ void DumpCFG::write_data(int n, double *mybuf)
fprintf(fp,"%s\n",typenames[itype]);
for (; i < nchosen; i++) {
if (rbuf[i][1] == itype) {
for (j = 2; j < size_one; j++) {
if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
else fprintf(fp,vformat[j],rbuf[i][j]);
}
if (unwrapflag == 0)
for (j = 2; j < size_one; j++) {
if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
else fprintf(fp,vformat[j],rbuf[i][j]);
}
else
// Unwrapped scaled coordinates are shifted to
// center of expanded box, to prevent
// rewrapping by AtomEye. Dividing by
// expansion factor restores correct
// interatomic distances.
for (j = 2; j < 5; j++) {
unwrap_coord = (rbuf[i][j] - 0.5)/UNWRAPEXPAND + 0.5;
fprintf(fp,vformat[j],unwrap_coord);
}
for (j = 5; j < size_one; j++) {
if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (rbuf[i][j]));
else fprintf(fp,vformat[j],rbuf[i][j]);
}
fprintf(fp,"\n");
}
}

1
src/dump_cfg.h
View File

@ -36,6 +36,7 @@ class DumpCFG : public DumpCustom {
int nchosen; // # of lines to be written on a writing proc
int nlines; // # of lines transferred from buf to rbuf
double **rbuf; // buf of data lines for data lines rearrangement
int unwrapflag; // 1 if unwrapped coordinates are requested
void init_style();
void write_header(bigint);

207
src/dump_custom.cpp
View File

@ -35,7 +35,9 @@ using namespace LAMMPS_NS;
// same list as in compute_property.cpp, also customize that command
enum{ID,MOL,TYPE,MASS,
X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,IX,IY,IZ,
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,
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
@ -563,6 +565,70 @@ int DumpCustom::count()
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XSU) {
double **x = atom->x;
int *image = atom->image;
double boxxlo = domain->boxlo[0];
double invxprd = 1.0/domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][0] - boxxlo) * invxprd + (image[i] & 1023) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSU) {
double **x = atom->x;
int *image = atom->image;
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;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSU) {
double **x = atom->x;
int *image = atom->image;
double boxzlo = domain->boxlo[2];
double invzprd = 1.0/domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][2] - boxzlo) * invzprd + (image[i] >> 20) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XSUTRI) {
double **x = atom->x;
int *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) +
h_inv[4]*(x[i][2]-boxlo[2]) +
(image[i] & 1023) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSUTRI) {
double **x = atom->x;
int *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
h_inv[3]*(x[i][2]-boxlo[2]) +
(image[i] >> 10 & 1023) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSUTRI) {
double **x = atom->x;
int *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]) +
(image[i] >> 20) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IX) {
int *image = atom->image;
for (i = 0; i < nlocal; i++)
@ -879,6 +945,18 @@ void DumpCustom::parse_fields(int narg, char **arg)
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zu_triclinic;
else pack_choice[i] = &DumpCustom::pack_zu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"xsu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xsu_triclinic;
else pack_choice[i] = &DumpCustom::pack_xsu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"ysu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ysu_triclinic;
else pack_choice[i] = &DumpCustom::pack_ysu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"zsu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zsu_triclinic;
else pack_choice[i] = &DumpCustom::pack_zsu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[i] = &DumpCustom::pack_ix;
vtype[i] = INT;
@ -1254,6 +1332,19 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = ZUTRI;
else if (strcmp(arg[1],"xsu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = XSU;
else if (strcmp(arg[1],"xsu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = XSUTRI;
else if (strcmp(arg[1],"ysu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = YSU;
else if (strcmp(arg[1],"ysu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = YSUTRI;
else if (strcmp(arg[1],"zsu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = ZSU;
else if (strcmp(arg[1],"zsu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = ZSUTRI;
else if (strcmp(arg[1],"ix") == 0) thresh_array[nthresh] = IX;
else if (strcmp(arg[1],"iy") == 0) thresh_array[nthresh] = IY;
else if (strcmp(arg[1],"iz") == 0) thresh_array[nthresh] = IZ;
@ -1821,6 +1912,120 @@ void DumpCustom::pack_zu_triclinic(int n)
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_xsu(int n)
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
double boxxlo = domain->boxlo[0];
double invxprd = 1.0/domain->xprd;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (x[i][0] - boxxlo) * invxprd + (image[i] & 1023) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_ysu(int n)
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
double boxylo = domain->boxlo[1];
double invyprd = 1.0/domain->yprd;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (x[i][1] - boxylo) * invyprd + (image[i] >> 10 & 1023) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_zsu(int n)
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
double boxzlo = domain->boxlo[2];
double invzprd = 1.0/domain->zprd;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (x[i][2] - boxzlo) * invzprd + (image[i] >> 20) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_xsu_triclinic(int n)
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) +
h_inv[4]*(x[i][2]-boxlo[2]) +
(image[i] & 1023) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_ysu_triclinic(int n)
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = h_inv[1]*(x[i][1]-boxlo[1]) +
h_inv[3]*(x[i][2]-boxlo[2]) +
(image[i] >> 10 & 1023) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_zsu_triclinic(int n)
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = h_inv[2]*(x[i][2]-boxlo[2]) +
(image[i] >> 20) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_ix(int n)
{
int *image = atom->image;