forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2455 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
b511b9febb
commit
216f4bb3f7
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@ -40,12 +40,6 @@ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
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void DumpAtom::init()
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{
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// this error check cannot occur in constructor since scale_flag = 1
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// is the default and it can be changed by dump_modify
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if (scale_flag && domain->triclinic)
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error->all("Cannot dump scaled coords with triclinic box");
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if (image_flag == 0) size_one = 5;
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else size_one = 8;
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@ -72,10 +66,14 @@ void DumpAtom::init()
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if (binary) header_choice = &DumpAtom::header_binary;
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else header_choice = &DumpAtom::header_item;
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if (scale_flag == 1 && image_flag == 0)
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if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0)
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pack_choice = &DumpAtom::pack_scale_noimage;
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else if (scale_flag == 1 && image_flag == 1)
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else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0)
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pack_choice = &DumpAtom::pack_scale_image;
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else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1)
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pack_choice = &DumpAtom::pack_scale_noimage_triclinic;
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else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1)
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pack_choice = &DumpAtom::pack_scale_image_triclinic;
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else if (scale_flag == 0 && image_flag == 0)
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pack_choice = &DumpAtom::pack_noscale_noimage;
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else if (scale_flag == 0 && image_flag == 1)
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@ -236,6 +234,62 @@ int DumpAtom::pack_scale_noimage()
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_scale_image_triclinic()
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{
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int *tag = atom->tag;
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int *type = atom->type;
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int *image = atom->image;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double lamda[3];
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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domain->x2lamda(x[i],lamda);
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buf[m++] = lamda[0];
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buf[m++] = lamda[1];
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buf[m++] = lamda[2];
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buf[m++] = (image[i] & 1023) - 512;
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buf[m++] = (image[i] >> 10 & 1023) - 512;
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buf[m++] = (image[i] >> 20) - 512;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_scale_noimage_triclinic()
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{
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double lamda[3];
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int m = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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buf[m++] = tag[i];
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buf[m++] = type[i];
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domain->x2lamda(x[i],lamda);
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buf[m++] = lamda[0];
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buf[m++] = lamda[1];
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buf[m++] = lamda[2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int DumpAtom::pack_noscale_image()
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{
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int *tag = atom->tag;
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@ -44,6 +44,8 @@ class DumpAtom : public Dump {
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int pack_scale_noimage();
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int pack_noscale_image();
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int pack_noscale_noimage();
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int pack_scale_image_triclinic();
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int pack_scale_noimage_triclinic();
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typedef void (DumpAtom::*FnPtrData)(int, double *);
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FnPtrData write_choice; // ptr to write data functions
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@ -32,7 +32,8 @@ using namespace LAMMPS_NS;
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// customize by adding keyword to 1st enum
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enum{ID,MOL,TYPE,MASS,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
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enum{ID,MOL,TYPE,MASS,
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X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,IX,IY,IZ,
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VX,VY,VZ,FX,FY,FZ,
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Q,MUX,MUY,MUZ,RADIUS,OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
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QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
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@ -352,6 +353,7 @@ int DumpCustom::count()
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ptr = atom->rmass;
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nstride = 1;
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}
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} else if (thresh_array[ithresh] == X) {
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ptr = &atom->x[0][0];
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nstride = 3;
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@ -361,6 +363,7 @@ int DumpCustom::count()
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} else if (thresh_array[ithresh] == Z) {
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ptr = &atom->x[0][2];
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nstride = 3;
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} else if (thresh_array[ithresh] == XS) {
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double **x = atom->x;
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double boxxlo = domain->boxlo[0];
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@ -385,6 +388,34 @@ int DumpCustom::count()
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dchoose[i] = (x[i][2] - boxzlo) * invzprd;
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == XSTRI) {
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double **x = atom->x;
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double *boxlo = domain->boxlo;
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double *h_inv = domain->h_inv;
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for (i = 0; i < nlocal; i++)
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dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
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h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == YSTRI) {
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double **x = atom->x;
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double *boxlo = domain->boxlo;
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double *h_inv = domain->h_inv;
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for (i = 0; i < nlocal; i++)
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dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
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h_inv[3]*(x[i][2]-boxlo[2]);
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == ZSTRI) {
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double **x = atom->x;
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double *boxlo = domain->boxlo;
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double *h_inv = domain->h_inv;
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for (i = 0; i < nlocal; i++)
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dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]);
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == XU) {
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double **x = atom->x;
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int *image = atom->image;
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@ -409,6 +440,44 @@ int DumpCustom::count()
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dchoose[i] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == XUTRI) {
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double **x = atom->x;
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int *image = atom->image;
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double *h = domain->h;
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int xbox,ybox,zbox;
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for (i = 0; i < nlocal; i++) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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dchoose[i] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
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}
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == YUTRI) {
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double **x = atom->x;
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int *image = atom->image;
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double *h = domain->h;
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int ybox,zbox;
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for (i = 0; i < nlocal; i++) {
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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dchoose[i] = x[i][1] + h[1]*ybox + h[3]*zbox;
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}
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == ZUTRI) {
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double **x = atom->x;
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int *image = atom->image;
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double *h = domain->h;
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int zbox;
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for (i = 0; i < nlocal; i++) {
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zbox = (image[i] >> 20) - 512;
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dchoose[i] = x[i][2] + h[2]*zbox;
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}
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == IX) {
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int *image = atom->image;
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for (i = 0; i < nlocal; i++)
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@ -427,6 +496,7 @@ int DumpCustom::count()
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dchoose[i] = (image[i] >> 20) - 512;
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ptr = dchoose;
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nstride = 1;
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} else if (thresh_array[ithresh] == VX) {
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ptr = &atom->v[0][0];
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nstride = 3;
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@ -685,28 +755,28 @@ void DumpCustom::parse_fields(int narg, char **arg)
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pack_choice[i] = &DumpCustom::pack_z;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"xs") == 0) {
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if (domain->triclinic)
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error->all("Cannot dump scaled coords with triclinic box");
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pack_choice[i] = &DumpCustom::pack_xs;
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if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xs_triclinic;
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else pack_choice[i] = &DumpCustom::pack_xs;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"ys") == 0) {
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if (domain->triclinic)
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error->all("Cannot dump scaled coords with triclinic box");
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pack_choice[i] = &DumpCustom::pack_ys;
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if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ys_triclinic;
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else pack_choice[i] = &DumpCustom::pack_ys;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"zs") == 0) {
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if (domain->triclinic)
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error->all("Cannot dump scaled coords with triclinic box");
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pack_choice[i] = &DumpCustom::pack_zs;
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if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zs_triclinic;
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else pack_choice[i] = &DumpCustom::pack_zs;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"xu") == 0) {
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pack_choice[i] = &DumpCustom::pack_xu;
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if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xu_triclinic;
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else pack_choice[i] = &DumpCustom::pack_xu;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"yu") == 0) {
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pack_choice[i] = &DumpCustom::pack_yu;
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if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_yu_triclinic;
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else pack_choice[i] = &DumpCustom::pack_yu;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"zu") == 0) {
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pack_choice[i] = &DumpCustom::pack_zu;
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if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zu_triclinic;
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else pack_choice[i] = &DumpCustom::pack_zu;
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vtype[i] = DOUBLE;
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} else if (strcmp(arg[iarg],"ix") == 0) {
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pack_choice[i] = &DumpCustom::pack_ix;
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@ -1043,13 +1113,6 @@ int DumpCustom::modify_param(int narg, char **arg)
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memory->srealloc(thresh_value,(nthresh+1)*sizeof(double),
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"dump:thresh_value");
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// error check for triclinic box
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if (domain->triclinic &&
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(strcmp(arg[1],"xs") == 0 || strcmp(arg[1],"ys") == 0 ||
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strcmp(arg[1],"zs") == 0))
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error->all("Cannot dump scaled coords with triclinic box");
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// set keyword type of threshhold
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// customize by adding to if statement
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@ -1057,15 +1120,37 @@ int DumpCustom::modify_param(int narg, char **arg)
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else if (strcmp(arg[1],"mol") == 0) thresh_array[nthresh] = MOL;
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else if (strcmp(arg[1],"type") == 0) thresh_array[nthresh] = TYPE;
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else if (strcmp(arg[1],"mass") == 0) thresh_array[nthresh] = MASS;
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else if (strcmp(arg[1],"x") == 0) thresh_array[nthresh] = X;
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else if (strcmp(arg[1],"y") == 0) thresh_array[nthresh] = Y;
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else if (strcmp(arg[1],"z") == 0) thresh_array[nthresh] = Z;
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else if (strcmp(arg[1],"xs") == 0) thresh_array[nthresh] = XS;
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else if (strcmp(arg[1],"ys") == 0) thresh_array[nthresh] = YS;
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else if (strcmp(arg[1],"zs") == 0) thresh_array[nthresh] = ZS;
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else if (strcmp(arg[1],"xu") == 0) thresh_array[nthresh] = XU;
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else if (strcmp(arg[1],"yu") == 0) thresh_array[nthresh] = YU;
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else if (strcmp(arg[1],"zu") == 0) thresh_array[nthresh] = ZU;
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else if (strcmp(arg[1],"xs") == 0 && domain->triclinic == 0)
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thresh_array[nthresh] = XS;
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else if (strcmp(arg[1],"xs") == 0 && domain->triclinic == 1)
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thresh_array[nthresh] = XSTRI;
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else if (strcmp(arg[1],"ys") == 0 && domain->triclinic == 0)
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thresh_array[nthresh] = YS;
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else if (strcmp(arg[1],"ys") == 0 && domain->triclinic == 1)
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thresh_array[nthresh] = YSTRI;
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else if (strcmp(arg[1],"zs") == 0 && domain->triclinic == 0)
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thresh_array[nthresh] = ZS;
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else if (strcmp(arg[1],"zs") == 0 && domain->triclinic == 1)
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thresh_array[nthresh] = ZSTRI;
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else if (strcmp(arg[1],"xu") == 0 && domain->triclinic == 0)
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thresh_array[nthresh] = XU;
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else if (strcmp(arg[1],"xu") == 0 && domain->triclinic == 1)
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thresh_array[nthresh] = XUTRI;
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else if (strcmp(arg[1],"yu") == 0 && domain->triclinic == 0)
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thresh_array[nthresh] = YU;
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else if (strcmp(arg[1],"yu") == 0 && domain->triclinic == 1)
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thresh_array[nthresh] = YUTRI;
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else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 0)
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thresh_array[nthresh] = ZU;
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else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 1)
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thresh_array[nthresh] = ZUTRI;
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else if (strcmp(arg[1],"ix") == 0) thresh_array[nthresh] = IX;
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else if (strcmp(arg[1],"iy") == 0) thresh_array[nthresh] = IY;
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else if (strcmp(arg[1],"iz") == 0) thresh_array[nthresh] = IZ;
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@ -1475,13 +1560,66 @@ void DumpCustom::pack_zs(int n)
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_xs_triclinic(int n)
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{
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double *boxlo = domain->boxlo;
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double *h_inv = domain->h_inv;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
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h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_ys_triclinic(int n)
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{
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double *boxlo = domain->boxlo;
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double *h_inv = domain->h_inv;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]);
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_zs_triclinic(int n)
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{
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double *boxlo = domain->boxlo;
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double *h_inv = domain->h_inv;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = h_inv[2]*(x[i][2]-boxlo[2]);
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n += size_one;
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustom::pack_xu(int n)
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{
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double **x = atom->x;
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int *image = atom->image;
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double xprd = domain->xprd;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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for (int i = 0; i < nlocal; i++)
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if (choose[i]) {
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buf[n] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
|
||||
|
|
@ -1495,9 +1633,10 @@ void DumpCustom::pack_yu(int n)
|
|||
{
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
double yprd = domain->yprd;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double yprd = domain->yprd;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (choose[i]) {
|
||||
buf[n] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
|
||||
|
|
@ -1511,9 +1650,10 @@ void DumpCustom::pack_zu(int n)
|
|||
{
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
double zprd = domain->zprd;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double zprd = domain->zprd;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (choose[i]) {
|
||||
buf[n] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
|
||||
|
|
@ -1523,6 +1663,66 @@ void DumpCustom::pack_zu(int n)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_xu_triclinic(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *h = domain->h;
|
||||
int xbox,ybox,zbox;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (choose[i]) {
|
||||
xbox = (image[i] & 1023) - 512;
|
||||
ybox = (image[i] >> 10 & 1023) - 512;
|
||||
zbox = (image[i] >> 20) - 512;
|
||||
buf[n] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_yu_triclinic(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *h = domain->h;
|
||||
int ybox,zbox;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (choose[i]) {
|
||||
ybox = (image[i] >> 10 & 1023) - 512;
|
||||
zbox = (image[i] >> 20) - 512;
|
||||
buf[n] = x[i][1] + h[1]*ybox + h[3]*zbox;
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_zu_triclinic(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *h = domain->h;
|
||||
int zbox;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (choose[i]) {
|
||||
zbox = (image[i] >> 20) - 512;
|
||||
buf[n] = x[i][2] + h[2]*zbox;
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_ix(int n)
|
||||
{
|
||||
int *image = atom->image;
|
||||
|
|
|
|||
|
|
@ -92,18 +92,26 @@ class DumpCustom : public Dump {
|
|||
void pack_molecule(int);
|
||||
void pack_type(int);
|
||||
void pack_mass(int);
|
||||
|
||||
void pack_x(int);
|
||||
void pack_y(int);
|
||||
void pack_z(int);
|
||||
void pack_xs(int);
|
||||
void pack_ys(int);
|
||||
void pack_zs(int);
|
||||
void pack_xs_triclinic(int);
|
||||
void pack_ys_triclinic(int);
|
||||
void pack_zs_triclinic(int);
|
||||
void pack_xu(int);
|
||||
void pack_yu(int);
|
||||
void pack_zu(int);
|
||||
void pack_xu_triclinic(int);
|
||||
void pack_yu_triclinic(int);
|
||||
void pack_zu_triclinic(int);
|
||||
void pack_ix(int);
|
||||
void pack_iy(int);
|
||||
void pack_iz(int);
|
||||
|
||||
void pack_vx(int);
|
||||
void pack_vy(int);
|
||||
void pack_vz(int);
|
||||
|
|
|
|||
Loading…
Reference in New Issue